11-67592132-T-G

Variant names:

• chr11-67592132-T-G
• rs596603

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 0.449 in 152,062 control chromosomes in the GnomAD database, including 18,011 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 0.45 (18011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68314 AN: 151944 Hom.: 18015 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.449 AC: 68317 AN: 152062 Hom.: 18011 Cov.: 32 AF XY: 0.457 AC XY: 33951 AN XY: 74292

African (AFR) AF: 0.159 AC: 6618 AN: 41530

American (AMR) AF: 0.436 AC: 6651 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2395 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3469 AN: 5174

South Asian (SAS) AF: 0.673 AC: 3231 AN: 4802

European-Finnish (FIN) AF: 0.564 AC: 5947 AN: 10546

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38277 AN: 67968

Other (OTH) AF: 0.486 AC: 1022 AN: 2104

Alfa AF: 0.421 Hom.: 5473

Bravo AF: 0.424

Asia WGS AF: 0.617 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.85
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs596603; hg19: chr11-67359603;