3-41087073-T-C

Variant names:

• chr3-41087073-T-C
• rs430727

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 0.553 in 151,944 control chromosomes in the GnomAD database, including 23,846 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 0.55 (23846 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83938 AN: 151826 Hom.: 23818 Cov.: 31

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.553 AC: 84016 AN: 151944 Hom.: 23846 Cov.: 31 AF XY: 0.546 AC XY: 40509 AN XY: 74246

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.546

Alfa AF: 0.545 Hom.: 24852

Bravo AF: 0.549

Asia WGS AF: 0.395 AC: 1377 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	1.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs430727; hg19: chr3-41128564;