11-68148630-C-T

Variant names:

• chr11-68148630-C-T
• rs2512623

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 0.518 in 151,848 control chromosomes in the GnomAD database, including 21,521 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 0.52 (21521 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 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: 0.519 AC: 78678 AN: 151730 Hom.: 21511 Cov.: 30

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.518 AC: 78706 AN: 151848 Hom.: 21521 Cov.: 30 AF XY: 0.525 AC XY: 38959 AN XY: 74204

African (AFR) AF: 0.329 AC: 13603 AN: 41406

American (AMR) AF: 0.644 AC: 9836 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2093 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3383 AN: 5148

South Asian (SAS) AF: 0.676 AC: 3248 AN: 4806

European-Finnish (FIN) AF: 0.589 AC: 6209 AN: 10544

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38473 AN: 67906

Other (OTH) AF: 0.559 AC: 1172 AN: 2096

Alfa AF: 0.379 Hom.: 1107

Bravo AF: 0.520

Asia WGS AF: 0.635 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.76
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs2512623; hg19: chr11-67916097;