rs10495147

chr1-220484221-A-G

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 0.687 in 152,150 control chromosomes in the GnomAD database, including 37,373 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 0.69 (37373 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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: 0.687 AC: 104490 AN: 152032 Hom.: 37374 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.687 AC: 104520 AN: 152150 Hom.: 37373 Cov.: 32 AF XY: 0.689 AC XY: 51240 AN XY: 74382

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.706

Alfa AF: 0.720 Hom.: 5023

Bravo AF: 0.664

Asia WGS AF: 0.617 AC: 2145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.3
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495147; hg19: chr1-220657563; COSMIC: COSV71682241;