chr10-95585932-A-C

Variant names:

• chr10-95585932-A-C
• rs495998

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 0.394 in 152,056 control chromosomes in the GnomAD database, including 14,445 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 0.39 (14445 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

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 (NFE) allele frequency at 95% confidence interval = 0.518 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: 0.395 AC: 59974 AN: 151938 Hom.: 14447 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.394 AC: 59972 AN: 152056 Hom.: 14445 Cov.: 31 AF XY: 0.393 AC XY: 29231 AN XY: 74318

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.367

Alfa AF: 0.446 Hom.: 2103

Bravo AF: 0.386

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs495998; hg19: chr10-97345689;