8-7041476-T-C

Variant names:

• chr8-7041476-T-C
• rs12716641

Variant summary

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

The variant allele was found at a frequency of 0.421 in 152,008 control chromosomes in the GnomAD database, including 14,040 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 0.42 (14040 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.421 AC: 64013 AN: 151890 Hom.: 14041 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.421 AC: 64041 AN: 152008 Hom.: 14040 Cov.: 32 AF XY: 0.424 AC XY: 31520 AN XY: 74300

African (AFR) AF: 0.295 AC: 12221 AN: 41442

American (AMR) AF: 0.437 AC: 6674 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3466

East Asian (EAS) AF: 0.246 AC: 1275 AN: 5176

South Asian (SAS) AF: 0.424 AC: 2042 AN: 4812

European-Finnish (FIN) AF: 0.510 AC: 5387 AN: 10554

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33216 AN: 67962

Other (OTH) AF: 0.440 AC: 928 AN: 2110

Alfa AF: 0.457 Hom.: 22071

Bravo AF: 0.409

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.29
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs12716641; hg19: chr8-6898998;