rs11230874

Positions:

• chr11-62028114-T-G

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 0.0746 in 152,040 control chromosomes in the GnomAD database, including 1,046 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 0.075 (1046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0745 AC: 11312 AN: 151922 Hom.: 1038 Cov.: 32

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.0974

Gnomad FIN AF: 0.0536

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.0775

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

GnomAD4 genome AF: 0.0746 AC: 11339 AN: 152040 Hom.: 1046 Cov.: 32 AF XY: 0.0809 AC XY: 6015 AN XY: 74320

Gnomad4 AFR AF: 0.0620

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.0979

Gnomad4 FIN AF: 0.0536

Gnomad4 NFE AF: 0.0317

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0520 Hom.: 65

Bravo AF: 0.0921

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11230874; hg19: chr11-61795586;