1-31408625-T-C

Variant names:

• chr1-31408625-T-C
• rs1039630

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 0.485 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.485 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

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.479

Alfa AF: 0.433 Hom.: 2915

Bravo AF: 0.486

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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