rs972164

Variant names:

• chr8-139391630-A-G
• rs972164

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 0.388 in 152,054 control chromosomes in the GnomAD database, including 13,440 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 0.39 (13440 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

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 = 0.632 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: 0.387 AC: 58871 AN: 151936 Hom.: 13418 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.388 AC: 58942 AN: 152054 Hom.: 13440 Cov.: 33 AF XY: 0.388 AC XY: 28815 AN XY: 74316

African (AFR) AF: 0.638 AC: 26467 AN: 41470

American (AMR) AF: 0.300 AC: 4591 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2667 AN: 5170

South Asian (SAS) AF: 0.318 AC: 1533 AN: 4814

European-Finnish (FIN) AF: 0.325 AC: 3430 AN: 10562

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18096 AN: 67966

Other (OTH) AF: 0.380 AC: 804 AN: 2114

Alfa AF: 0.294 Hom.: 3783

Bravo AF: 0.400

Asia WGS AF: 0.416 AC: 1450 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	0.28
DANN	Benign	0.37
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs972164; hg19: chr8-140403873;