rs10895458

Variant names:

• chr11-103547356-A-C
• rs10895458

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.187 AC: 7762 AN: 41512

American (AMR) AF: 0.327 AC: 4998 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3466

East Asian (EAS) AF: 0.158 AC: 816 AN: 5174

South Asian (SAS) AF: 0.396 AC: 1912 AN: 4828

European-Finnish (FIN) AF: 0.516 AC: 5452 AN: 10570

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34299 AN: 67978

Other (OTH) AF: 0.423 AC: 891 AN: 2108

Alfa AF: 0.472 Hom.: 30243

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10895458; hg19: chr11-103418084;