rs614367

Variant names:

• chr11-69513996-C-T
• rs614367

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 0.135 in 152,136 control chromosomes in the GnomAD database, including 1,512 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 0.13 (1512 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867
• Publications: 108 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20500 AN: 152018 Hom.: 1512 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00830

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.135 AC: 20512 AN: 152136 Hom.: 1512 Cov.: 31 AF XY: 0.136 AC XY: 10132 AN XY: 74370

African (AFR) AF: 0.128 AC: 5332 AN: 41512

American (AMR) AF: 0.0889 AC: 1357 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3472

East Asian (EAS) AF: 0.00793 AC: 41 AN: 5170

South Asian (SAS) AF: 0.163 AC: 785 AN: 4824

European-Finnish (FIN) AF: 0.174 AC: 1843 AN: 10580

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.151 AC: 10241 AN: 68000

Other (OTH) AF: 0.134 AC: 282 AN: 2110

Alfa AF: 0.140 Hom.: 7311

Bravo AF: 0.124

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.35
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs614367; hg19: chr11-69328764;