15-67811049-T-C

Variant names:

• chr15-67811049-T-C
• rs4776377

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 0.388 in 152,158 control chromosomes in the GnomAD database, including 12,317 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 0.39 (12317 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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: 0.388 AC: 59024 AN: 152040 Hom.: 12278 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.388 AC: 59109 AN: 152158 Hom.: 12317 Cov.: 33 AF XY: 0.393 AC XY: 29249 AN XY: 74390

African (AFR) AF: 0.423 AC: 17544 AN: 41500

American (AMR) AF: 0.538 AC: 8238 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1570 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3602 AN: 5172

South Asian (SAS) AF: 0.449 AC: 2171 AN: 4830

European-Finnish (FIN) AF: 0.302 AC: 3190 AN: 10574

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21667 AN: 67992

Other (OTH) AF: 0.402 AC: 849 AN: 2114

Alfa AF: 0.349 Hom.: 1656

Bravo AF: 0.411

Asia WGS AF: 0.563 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.9
DANN	Benign	0.80
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs4776377; hg19: chr15-68103387;