rs10895458

Variant names:

• chr11-103547356-A-C
• rs10895458

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 0.385 in 152,122 control chromosomes in the GnomAD database, including 12,963 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 0.38 (12963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 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: 0.385 AC: 58552 AN: 152004 Hom.: 12964 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.385 AC: 58558 AN: 152122 Hom.: 12963 Cov.: 32 AF XY: 0.383 AC XY: 28480 AN XY: 74358

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.423

Alfa AF: 0.484 Hom.: 24861

Bravo AF: 0.362

Asia WGS AF: 0.284 AC: 987 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10895458; hg19: chr11-103418084;