rs1403637

Positions:

• chr3-172440607-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 0.297 in 152,080 control chromosomes in the GnomAD database, including 8,002 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 0.30 (8002 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 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: 0.297 AC: 45172 AN: 151962 Hom.: 8005 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.297 AC: 45160 AN: 152080 Hom.: 8002 Cov.: 31 AF XY: 0.293 AC XY: 21753 AN XY: 74340

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.347

Alfa AF: 0.391 Hom.: 23146

Bravo AF: 0.287

Asia WGS AF: 0.181 AC: 634 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.10
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1403637; hg19: chr3-172158397;