rs10749902

Variant names:

• chr11-107324855-C-T
• rs10749902

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 0.266 in 151,884 control chromosomes in the GnomAD database, including 5,616 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 (5616 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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: 0.266 AC: 40354 AN: 151764 Hom.: 5621 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.266 AC: 40359 AN: 151884 Hom.: 5616 Cov.: 31 AF XY: 0.262 AC XY: 19473 AN XY: 74232

African (AFR) AF: 0.210 AC: 8712 AN: 41440

American (AMR) AF: 0.200 AC: 3045 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1156 AN: 3466

East Asian (EAS) AF: 0.279 AC: 1433 AN: 5142

South Asian (SAS) AF: 0.282 AC: 1355 AN: 4802

European-Finnish (FIN) AF: 0.275 AC: 2893 AN: 10536

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20946 AN: 67918

Other (OTH) AF: 0.260 AC: 549 AN: 2112

Alfa AF: 0.288 Hom.: 10994

Bravo AF: 0.254

Asia WGS AF: 0.249 AC: 865 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	2.4
DANN	Benign	0.70
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10749902; hg19: chr11-107195581;