rs1270629

Variant names:

• chr14-93180064-T-C
• rs1270629

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.929 AC: 38320 AN: 41266

American (AMR) AF: 0.726 AC: 11016 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2347 AN: 3466

East Asian (EAS) AF: 0.722 AC: 3714 AN: 5146

South Asian (SAS) AF: 0.814 AC: 3906 AN: 4798

European-Finnish (FIN) AF: 0.709 AC: 7353 AN: 10364

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.740 AC: 50259 AN: 67938

Other (OTH) AF: 0.780 AC: 1642 AN: 2104

Alfa AF: 0.753 Hom.: 39929

Bravo AF: 0.799

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1270629; hg19: chr14-93646409;