rs6819681

Variant names:

• chr4-60542358-T-C
• rs6819681

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 0.0878 in 152,088 control chromosomes in the GnomAD database, including 635 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 0.088 (635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 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: 0.0877 AC: 13330 AN: 151970 Hom.: 628 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0619

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0878 AC: 13353 AN: 152088 Hom.: 635 Cov.: 32 AF XY: 0.0882 AC XY: 6556 AN XY: 74328

African (AFR) AF: 0.0965 AC: 4007 AN: 41534

American (AMR) AF: 0.0620 AC: 945 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3470

East Asian (EAS) AF: 0.110 AC: 564 AN: 5128

South Asian (SAS) AF: 0.123 AC: 595 AN: 4826

European-Finnish (FIN) AF: 0.0849 AC: 902 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0871 AC: 5916 AN: 67948

Other (OTH) AF: 0.0792 AC: 167 AN: 2108

Alfa AF: 0.0936 Hom.: 79

Bravo AF: 0.0843

Asia WGS AF: 0.123 AC: 429 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.76
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs6819681; hg19: chr4-61408076;