chr15-75665034-T-C

Variant names:

• chr15-75665034-T-C
• rs4886727

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 0.897 in 152,234 control chromosomes in the GnomAD database, including 61,872 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 0.90 (61872 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136505 AN: 152118 Hom.: 61824 Cov.: 32

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.897 AC: 136607 AN: 152234 Hom.: 61872 Cov.: 32 AF XY: 0.891 AC XY: 66330 AN XY: 74414

African (AFR) AF: 0.971 AC: 40321 AN: 41542

American (AMR) AF: 0.823 AC: 12578 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3070 AN: 3472

East Asian (EAS) AF: 0.521 AC: 2688 AN: 5162

South Asian (SAS) AF: 0.819 AC: 3950 AN: 4822

European-Finnish (FIN) AF: 0.876 AC: 9277 AN: 10592

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61763 AN: 68034

Other (OTH) AF: 0.874 AC: 1849 AN: 2116

Alfa AF: 0.898 Hom.: 99117

Bravo AF: 0.891

Asia WGS AF: 0.717 AC: 2494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.73
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4886727; hg19: chr15-75957375;