rs4257844

chr6-66925791-T-C

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 0.779 in 152,046 control chromosomes in the GnomAD database, including 47,165 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 0.78 (47165 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.87 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: 0.779 AC: 118359 AN: 151928 Hom.: 47147 Cov.: 31

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.779 AC: 118418 AN: 152046 Hom.: 47165 Cov.: 31 AF XY: 0.768 AC XY: 57096 AN XY: 74328

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.775

Alfa AF: 0.847 Hom.: 91687

Bravo AF: 0.766

Asia WGS AF: 0.472 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.6
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4257844; hg19: chr6-67635684;