11-67579272-T-C

Variant names:

• chr11-67579272-T-C
• rs7927381

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 0.81 in 151,980 control chromosomes in the GnomAD database, including 51,033 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 0.81 (51033 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.908 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: 0.810 AC: 123066 AN: 151862 Hom.: 51031 Cov.: 30

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.810 AC: 123118 AN: 151980 Hom.: 51033 Cov.: 30 AF XY: 0.808 AC XY: 60051 AN XY: 74280

African (AFR) AF: 0.647 AC: 26807 AN: 41408

American (AMR) AF: 0.691 AC: 10545 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3129 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4359 AN: 5160

South Asian (SAS) AF: 0.919 AC: 4424 AN: 4812

European-Finnish (FIN) AF: 0.838 AC: 8848 AN: 10560

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62133 AN: 68006

Other (OTH) AF: 0.834 AC: 1760 AN: 2110

Alfa AF: 0.796 Hom.: 28542

Bravo AF: 0.789

Asia WGS AF: 0.867 AC: 3016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.35
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs7927381; hg19: chr11-67346743;