rs34935416

Variant names:

• chr19-49054626-A-G
• rs34935416
• NM_001385261.1:c.184-21T>C

Your query was ambiguous. Multiple possible variants found:

• chr19-49054626-A-G
• chr19-49054626-A-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001385261.1(CGB7):​c.184-21T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.048 (91 hom., cov: 17)
  • Exomes 𝑓: 0.087 (7210 hom.)
  • Failed GnomAD Quality Control
• Consequence: CGB7 NM_001385261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 1 publications found

Genes affected

CGB7 (HGNC:16451): (chorionic gonadotropin subunit beta 7) This gene is a member of the glycoprotein hormone beta chain family and encodes the beta 7 subunit of chorionic gonadotropin (CG). Glycoprotein hormones are heterodimers consisting of a common alpha subunit and an unique beta subunit which confers biological specificity. CG is produced by the trophoblastic cells of the placenta and stimulates the ovaries to synthesize the steroids that are essential for the maintenance of pregnancy. The beta subunit of CG is encoded by 6 genes which are arranged in tandem and inverted pairs on chromosome 19q13.3 and contiguous with the luteinizing hormone beta subunit gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CGB7	NM_001385261.1	c.184-21T>C		intron_variant	Intron 4 of 4	ENST00000684222.1	NP_001372190.1
CGB7	NM_033142.2	c.184-21T>C		intron_variant	Intron 4 of 4		NP_149133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CGB7	ENST00000684222.1	c.184-21T>C		intron_variant	Intron 4 of 4		NM_001385261.1	ENSP00000507822.1
CGB7	ENST00000596965.5	c.184-21T>C		intron_variant	Intron 4 of 4	2		ENSP00000469076.1
CGB7	ENST00000597853.5	c.184-21T>C		intron_variant	Intron 4 of 4	2		ENSP00000470813.1

Frequencies

GnomAD3 genomes AF: 0.0483 AC: 5521 AN: 114288 Hom.: 91 Cov.: 17

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.0118

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.0577

Gnomad SAS AF: 0.0500

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.0699

Gnomad NFE AF: 0.0554

Gnomad OTH AF: 0.0523

GnomAD2 exomes AF: 0.151 AC: 8413 AN: 55862 AF XY: 0.157

Gnomad AFR exome AF: 0.128

Gnomad AMR exome AF: 0.104

Gnomad ASJ exome AF: 0.127

Gnomad EAS exome AF: 0.154

Gnomad FIN exome AF: 0.202

Gnomad NFE exome AF: 0.177

Gnomad OTH exome AF: 0.158

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0868 AC: 73177 AN: 843144 Hom.: 7210 Cov.: 13 AF XY: 0.0895 AC XY: 37717 AN XY: 421310

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0773 AC: 1685 AN: 21804

American (AMR) AF: 0.0609 AC: 1639 AN: 26902

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 1494 AN: 16948

East Asian (EAS) AF: 0.0925 AC: 2844 AN: 30742

South Asian (SAS) AF: 0.122 AC: 6833 AN: 55976

European-Finnish (FIN) AF: 0.172 AC: 4609 AN: 26746

Middle Eastern (MID) AF: 0.0965 AC: 263 AN: 2724

European-Non Finnish (NFE) AF: 0.0803 AC: 50041 AN: 622912

Other (OTH) AF: 0.0982 AC: 3769 AN: 38390

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0483 AC: 5520 AN: 114364 Hom.: 91 Cov.: 17 AF XY: 0.0442 AC XY: 2427 AN XY: 54930

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0466 AC: 1480 AN: 31752

American (AMR) AF: 0.0340 AC: 409 AN: 12030

Ashkenazi Jewish (ASJ) AF: 0.0450 AC: 127 AN: 2824

East Asian (EAS) AF: 0.0582 AC: 229 AN: 3938

South Asian (SAS) AF: 0.0493 AC: 168 AN: 3406

European-Finnish (FIN) AF: 0.0267 AC: 185 AN: 6918

Middle Eastern (MID) AF: 0.0600 AC: 15 AN: 250

European-Non Finnish (NFE) AF: 0.0554 AC: 2815 AN: 50830

Other (OTH) AF: 0.0523 AC: 82 AN: 1568

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0525 Hom.: 126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.22
PhyloP100		0.092
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34935416; hg19: chr19-49557883; COSMIC: COSV62281703; COSMIC: COSV62281703;