rs6631

Variant names:

• chr6-87085541-A-C
• rs6631
• NM_000735.4:c.*215T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-87085541-A-C
• chr6-87085541-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000735.4(CGA):​c.*215T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CGA NM_000735.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.63
• Publications: 15 publications found

Genes affected

CGA (HGNC:1885): (glycoprotein hormones, alpha polypeptide) The four human glycoprotein hormones chorionic gonadotropin (CG), luteinizing hormone (LH), follicle stimulating hormone (FSH), and thyroid stimulating hormone (TSH) are dimers consisting of alpha and beta subunits that are associated noncovalently. The alpha subunits of these hormones are identical, however, their beta chains are unique and confer biological specificity. The protein encoded by this gene is the alpha subunit and belongs to the glycoprotein hormones alpha chain family. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CGA	NM_000735.4	c.*215T>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000627148.3	NP_000726.1
CGA	NM_001252383.2	c.*215T>G		3_prime_UTR_variant	Exon 5 of 5		NP_001239312.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CGA	ENST00000627148.3	c.*215T>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_000735.4	ENSP00000486024.1
CGA	ENST00000369582.6	c.*215T>G		3_prime_UTR_variant	Exon 5 of 5	5		ENSP00000358595.3
CGA	ENST00000610310.3	c.*215T>G		downstream_gene_variant		3		ENSP00000482232.1
CGA	ENST00000630630.2	c.*676T>G		downstream_gene_variant		2		ENSP00000487300.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 336812 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 177246

African (AFR) AF: 0.00 AC: 0 AN: 10006

American (AMR) AF: 0.00 AC: 0 AN: 13636

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10226

East Asian (EAS) AF: 0.00 AC: 0 AN: 23004

South Asian (SAS) AF: 0.00 AC: 0 AN: 33670

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25344

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1434

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 200148

Other (OTH) AF: 0.00 AC: 0 AN: 19344

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.5
DANN	Benign	0.81
PhyloP100		2.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs6631; hg19: chr6-87795259;