chr11-62028114-T-G

Variant names:

• chr11-62028114-T-G
• rs11230874

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 0.0746 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0620 AC: 2574 AN: 41486

American (AMR) AF: 0.201 AC: 3062 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2297 AN: 5128

South Asian (SAS) AF: 0.0979 AC: 472 AN: 4820

European-Finnish (FIN) AF: 0.0536 AC: 568 AN: 10592

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0317 AC: 2153 AN: 67970

Other (OTH) AF: 0.0762 AC: 161 AN: 2112

Alfa AF: 0.0359 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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11230874; hg19: chr11-61795586;