rs437943

Positions:

• chr4-35370476-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 0.465 in 152,092 control chromosomes in the GnomAD database, including 18,980 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 0.46 (18980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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 (AFR) allele frequency at 95% confidence interval = 0.742 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: 0.464 AC: 70559 AN: 151972 Hom.: 18935 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.465 AC: 70663 AN: 152092 Hom.: 18980 Cov.: 32 AF XY: 0.461 AC XY: 34250 AN XY: 74350

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.412

Alfa AF: 0.360 Hom.: 22651

Bravo AF: 0.485

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.26
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: rs437943; hg19: chr4-35372098;