chr7-20007952-A-C

Variant names:

• chr7-20007952-A-C
• rs38152
• ENST00000415499.6:n.211+20967T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415499.6(ENSG00000243004):​n.211+20967T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,148 control chromosomes in the GnomAD database, including 599 homozygotes. 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 0.060 (599 hom., cov: 32)
• Consequence: ENSG00000243004 ENST00000415499.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 7 publications found

Genes affected

ENSG00000243004 (HGNC:58196):

ENSG00000296332 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MACC1-OT1	NR_110114.1	n.210+20967T>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243004	ENST00000415499.6	n.211+20967T>G		intron_variant	Intron 3 of 5	3
ENSG00000243004	ENST00000418442.1	n.340-600T>G		intron_variant	Intron 5 of 5	3
ENSG00000243004	ENST00000435968.5	n.158+20967T>G		intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes AF: 0.0595 AC: 9046 AN: 152030 Hom.: 597 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00415

Gnomad FIN AF: 0.00961

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0196

Gnomad OTH AF: 0.0589

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0596 AC: 9064 AN: 152148 Hom.: 599 Cov.: 32 AF XY: 0.0573 AC XY: 4259 AN XY: 74384

African (AFR) AF: 0.161 AC: 6655 AN: 41448

American (AMR) AF: 0.0429 AC: 655 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 148 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00436 AC: 21 AN: 4820

European-Finnish (FIN) AF: 0.00961 AC: 102 AN: 10618

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0196 AC: 1331 AN: 68018

Other (OTH) AF: 0.0578 AC: 122 AN: 2112

Alfa AF: 0.0305 Hom.: 730

Bravo AF: 0.0672

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs38152; hg19: chr7-20047575;