rs1144036

Variant names:

• chr11-116713705-T-C
• rs1144036

Your query was ambiguous. Multiple possible variants found:

• chr11-116713705-T-C
• chr11-116713705-T-G

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 0.0982 in 151,810 control chromosomes in the GnomAD database, including 965 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 (965 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 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: 0.0983 AC: 14909 AN: 151690 Hom.: 966 Cov.: 33

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0223

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0982 AC: 14908 AN: 151810 Hom.: 965 Cov.: 33 AF XY: 0.0948 AC XY: 7039 AN XY: 74216

African (AFR) AF: 0.0311 AC: 1279 AN: 41180

American (AMR) AF: 0.0903 AC: 1381 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3468

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0226 AC: 109 AN: 4830

European-Finnish (FIN) AF: 0.132 AC: 1391 AN: 10550

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10014 AN: 67998

Other (OTH) AF: 0.116 AC: 245 AN: 2110

Alfa AF: 0.114 Hom.: 1272

Bravo AF: 0.0928

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.50
DANN	Benign	0.52
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1144036; hg19: chr11-116584421;