rs1270629

Variant names:

• chr14-93180064-T-C
• rs1270629

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 0.789 in 151,450 control chromosomes in the GnomAD database, including 47,807 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 0.79 (47807 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 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: 0.789 AC: 119412 AN: 151332 Hom.: 47753 Cov.: 28

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.789 AC: 119525 AN: 151450 Hom.: 47807 Cov.: 28 AF XY: 0.784 AC XY: 57943 AN XY: 73926

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.780

Alfa AF: 0.740 Hom.: 27052

Bravo AF: 0.799

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1270629; hg19: chr14-93646409;