rs11910746

Variant names:

• chr21-31024249-G-A
• rs11910746

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.104 in 152,214 control chromosomes in the GnomAD database, including 1,312 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 0.10 (1312 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 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: 0.104 AC: 15753 AN: 152096 Hom.: 1307 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.0635

Gnomad SAS AF: 0.0762

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0422

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.104 AC: 15788 AN: 152214 Hom.: 1312 Cov.: 32 AF XY: 0.105 AC XY: 7835 AN XY: 74424

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.0640

Gnomad4 SAS AF: 0.0763

Gnomad4 FIN AF: 0.0357

Gnomad4 NFE AF: 0.0422

Gnomad4 OTH AF: 0.0941

Alfa AF: 0.0739 Hom.: 134

Bravo AF: 0.120

Asia WGS AF: 0.0780 AC: 273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11910746; hg19: chr21-32396568;