rs1270629

Positions:

• chr14-93180064-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 0.789 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;