chr1-25039556-T-A

Position:

• chr1-25039556-T-A

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 0.548 in 151,684 control chromosomes in the GnomAD database, including 22,829 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 0.55 (22829 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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: 0.548 AC: 83087 AN: 151566 Hom.: 22821 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.548 AC: 83119 AN: 151684 Hom.: 22829 Cov.: 31 AF XY: 0.549 AC XY: 40677 AN XY: 74122

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.572

Alfa AF: 0.542 Hom.: 2661

Bravo AF: 0.550

Asia WGS AF: 0.664 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs395376; hg19: chr1-25366047; COSMIC: COSV69619390;