rs6856651

chr4-72030740-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.424

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.39
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6856651; hg19: chr4-72896457;