rs10193895

Variant names:

• chr2-105653155-A-G
• rs10193895

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 0.0418 in 152,342 control chromosomes in the GnomAD database, including 174 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 0.042 (174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 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: 0.0418 AC: 6366 AN: 152224 Hom.: 174 Cov.: 32

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0201

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0328

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0418 AC: 6371 AN: 152342 Hom.: 174 Cov.: 32 AF XY: 0.0431 AC XY: 3212 AN XY: 74490

Gnomad4 AFR AF: 0.0509

Gnomad4 AMR AF: 0.0200

Gnomad4 ASJ AF: 0.0455

Gnomad4 EAS AF: 0.0825

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0328

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0327 Hom.: 95

Bravo AF: 0.0384

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.084
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10193895; hg19: chr2-106269612;