rs6856651

Variant names:

• chr4-72030740-A-T
• rs6856651

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 0.41 in 152,004 control chromosomes in the GnomAD database, including 13,915 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 0.41 (13915 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62183 AN: 151886 Hom.: 13874 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.410 AC: 62280 AN: 152004 Hom.: 13915 Cov.: 33 AF XY: 0.409 AC XY: 30398 AN XY: 74304

African (AFR) AF: 0.568 AC: 23520 AN: 41430

American (AMR) AF: 0.411 AC: 6279 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3464

East Asian (EAS) AF: 0.675 AC: 3489 AN: 5170

South Asian (SAS) AF: 0.459 AC: 2210 AN: 4814

European-Finnish (FIN) AF: 0.274 AC: 2894 AN: 10576

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21086 AN: 67952

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.355 Hom.: 1283

Bravo AF: 0.428

Asia WGS AF: 0.586 AC: 2037 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.39
DANN	Benign	0.49
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6856651; hg19: chr4-72896457;