rs3894944

chr4-7157975-G-Achr4-7157975-G-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 0.782 in 152,150 control chromosomes in the GnomAD database, including 46,541 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 (46541 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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: 0.782 AC: 118873 AN: 152032 Hom.: 46497 Cov.: 33

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.782 AC: 118976 AN: 152150 Hom.: 46541 Cov.: 33 AF XY: 0.786 AC XY: 58485 AN XY: 74370

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.784

Alfa AF: 0.784 Hom.: 7541

Bravo AF: 0.781

Asia WGS AF: 0.784 AC: 2730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.70
Dann	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3894944; hg19: chr4-7159702;