1-31408625-T-C

Variant names:

• chr1-31408625-T-C
• rs1039630

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 0.485 in 150,908 control chromosomes in the GnomAD database, including 18,277 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 0.49 (18277 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 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: 0.485 AC: 73155 AN: 150794 Hom.: 18229 Cov.: 29

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.485 AC: 73259 AN: 150908 Hom.: 18277 Cov.: 29 AF XY: 0.492 AC XY: 36205 AN XY: 73654

African (AFR) AF: 0.557 AC: 22894 AN: 41122

American (AMR) AF: 0.474 AC: 7191 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1495 AN: 3464

East Asian (EAS) AF: 0.669 AC: 3374 AN: 5046

South Asian (SAS) AF: 0.645 AC: 3073 AN: 4764

European-Finnish (FIN) AF: 0.477 AC: 4920 AN: 10322

Middle Eastern (MID) AF: 0.486 AC: 138 AN: 284

European-Non Finnish (NFE) AF: 0.423 AC: 28661 AN: 67712

Other (OTH) AF: 0.479 AC: 1005 AN: 2100

Alfa AF: 0.430 Hom.: 3059

Bravo AF: 0.486

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.63
PhyloP100		0.034

Splicing

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

Other links and lift over

dbSNP: rs1039630; hg19: chr1-31881472; COSMIC: COSV65489767;