rs11187549

Variant names:

• chr10-93604867-A-G
• rs11187549

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 0.0983 in 152,326 control chromosomes in the GnomAD database, including 1,390 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 0.098 (1390 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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: 0.0984 AC: 14981 AN: 152208 Hom.: 1394 Cov.: 33

Gnomad AFR AF: 0.0403

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0953

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0983 AC: 14973 AN: 152326 Hom.: 1390 Cov.: 33 AF XY: 0.105 AC XY: 7814 AN XY: 74492

African (AFR) AF: 0.0403 AC: 1674 AN: 41580

American (AMR) AF: 0.0692 AC: 1059 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3468

East Asian (EAS) AF: 0.484 AC: 2507 AN: 5180

South Asian (SAS) AF: 0.335 AC: 1620 AN: 4830

European-Finnish (FIN) AF: 0.0874 AC: 928 AN: 10620

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0953 AC: 6483 AN: 68028

Other (OTH) AF: 0.0936 AC: 198 AN: 2116

Alfa AF: 0.110 Hom.: 521

Bravo AF: 0.0904

Asia WGS AF: 0.337 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.70
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11187549; hg19: chr10-95364624;