rs6840776

Variant names:

• chr4-91738603-T-A
• rs6840776

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 0.673 in 151,958 control chromosomes in the GnomAD database, including 35,372 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 0.67 (35372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.769 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: 0.673 AC: 102170 AN: 151836 Hom.: 35358 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.673 AC: 102227 AN: 151958 Hom.: 35372 Cov.: 32 AF XY: 0.661 AC XY: 49081 AN XY: 74248

African (AFR) AF: 0.776 AC: 32156 AN: 41454

American (AMR) AF: 0.560 AC: 8526 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2379 AN: 3464

East Asian (EAS) AF: 0.207 AC: 1070 AN: 5166

South Asian (SAS) AF: 0.585 AC: 2825 AN: 4826

European-Finnish (FIN) AF: 0.570 AC: 6008 AN: 10540

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47003 AN: 67950

Other (OTH) AF: 0.669 AC: 1416 AN: 2116

Alfa AF: 0.685 Hom.: 4473

Bravo AF: 0.674

Asia WGS AF: 0.446 AC: 1543 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.4
DANN	Benign	0.38
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs6840776; hg19: chr4-92659754;