chr6-78691696-T-C

Variant names:

• chr6-78691696-T-C
• rs639370

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 0.639 in 152,048 control chromosomes in the GnomAD database, including 31,473 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 0.64 (31473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 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: 0.640 AC: 97173 AN: 151930 Hom.: 31468 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.639 AC: 97212 AN: 152048 Hom.: 31473 Cov.: 32 AF XY: 0.639 AC XY: 47496 AN XY: 74318

African (AFR) AF: 0.568 AC: 23543 AN: 41448

American (AMR) AF: 0.593 AC: 9050 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3472

East Asian (EAS) AF: 0.488 AC: 2530 AN: 5180

South Asian (SAS) AF: 0.618 AC: 2975 AN: 4816

European-Finnish (FIN) AF: 0.710 AC: 7510 AN: 10572

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.696 AC: 47349 AN: 67982

Other (OTH) AF: 0.645 AC: 1362 AN: 2112

Alfa AF: 0.665 Hom.: 87222

Bravo AF: 0.629

Asia WGS AF: 0.526 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.58
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs639370; hg19: chr6-79401413;