chr11-68141915-G-T

Variant names:

• chr11-68141915-G-T
• rs11228145

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 0.467 in 152,018 control chromosomes in the GnomAD database, including 19,639 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 0.47 (19639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 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: 0.467 AC: 70976 AN: 151900 Hom.: 19629 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.467 AC: 70987 AN: 152018 Hom.: 19639 Cov.: 32 AF XY: 0.475 AC XY: 35315 AN XY: 74274

African (AFR) AF: 0.146 AC: 6042 AN: 41490

American (AMR) AF: 0.626 AC: 9553 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2108 AN: 3468

East Asian (EAS) AF: 0.666 AC: 3432 AN: 5154

South Asian (SAS) AF: 0.678 AC: 3268 AN: 4818

European-Finnish (FIN) AF: 0.591 AC: 6231 AN: 10550

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38561 AN: 67962

Other (OTH) AF: 0.521 AC: 1099 AN: 2108

Alfa AF: 0.504 Hom.: 2663

Bravo AF: 0.461

Asia WGS AF: 0.628 AC: 2184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.47
DANN	Benign	0.69
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs11228145; hg19: chr11-67909382;