rs10749971

Variant names:

• chr11-111318433-A-G
• rs10749971

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 0.267 in 152,160 control chromosomes in the GnomAD database, including 6,342 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 0.27 (6342 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 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: 0.267 AC: 40558 AN: 152042 Hom.: 6341 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.267 AC: 40570 AN: 152160 Hom.: 6342 Cov.: 32 AF XY: 0.262 AC XY: 19497 AN XY: 74396

African (AFR) AF: 0.124 AC: 5160 AN: 41516

American (AMR) AF: 0.285 AC: 4358 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3466

East Asian (EAS) AF: 0.0722 AC: 374 AN: 5180

South Asian (SAS) AF: 0.179 AC: 865 AN: 4824

European-Finnish (FIN) AF: 0.275 AC: 2907 AN: 10584

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24703 AN: 67980

Other (OTH) AF: 0.297 AC: 627 AN: 2112

Alfa AF: 0.338 Hom.: 17723

Bravo AF: 0.265

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	19
DANN	Benign	0.79
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10749971; hg19: chr11-111189158;