rs1472962

Positions:

• chr4-94671226-G-A

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 0.612 in 152,064 control chromosomes in the GnomAD database, including 29,127 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 0.61 (29127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92987 AN: 151946 Hom.: 29094 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.612 AC: 93071 AN: 152064 Hom.: 29127 Cov.: 32 AF XY: 0.604 AC XY: 44924 AN XY: 74320

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.608

Alfa AF: 0.590 Hom.: 9827

Bravo AF: 0.627

Asia WGS AF: 0.482 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472962; hg19: chr4-95592377;