rs38664

Variant names:

• chr7-76761653-T-C
• rs38664

Your query was ambiguous. Multiple possible variants found:

• chr7-76761653-T-C
• chr7-76761653-T-G

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 0.68 in 152,006 control chromosomes in the GnomAD database, including 36,698 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 0.68 (36698 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.881 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: 0.679 AC: 103173 AN: 151886 Hom.: 36627 Cov.: 31

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.680 AC: 103304 AN: 152006 Hom.: 36698 Cov.: 31 AF XY: 0.679 AC XY: 50445 AN XY: 74302

African (AFR) AF: 0.889 AC: 36879 AN: 41482

American (AMR) AF: 0.720 AC: 11000 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2290 AN: 3466

East Asian (EAS) AF: 0.488 AC: 2516 AN: 5160

South Asian (SAS) AF: 0.692 AC: 3330 AN: 4814

European-Finnish (FIN) AF: 0.516 AC: 5453 AN: 10568

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39684 AN: 67924

Other (OTH) AF: 0.687 AC: 1449 AN: 2110

Alfa AF: 0.604 Hom.: 11938

Bravo AF: 0.703

Asia WGS AF: 0.624 AC: 2169 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	1.7
DANN	Benign	0.30
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs38664; hg19: chr7-76390970;