rs10895458

chr11-103547356-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;