rs7631540

Variant names:

• chr3-114111672-C-T
• rs7631540

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 0.393 in 152,122 control chromosomes in the GnomAD database, including 13,337 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 0.39 (13337 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906

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 (AMR) allele frequency at 95% confidence interval = 0.517 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: 0.393 AC: 59736 AN: 152002 Hom.: 13336 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.393 AC: 59736 AN: 152122 Hom.: 13337 Cov.: 33 AF XY: 0.399 AC XY: 29692 AN XY: 74348

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.449

Alfa AF: 0.463 Hom.: 33824

Bravo AF: 0.382

Asia WGS AF: 0.413 AC: 1434 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	0.49
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7631540; hg19: chr3-113830519;