chr15-59737814-C-T

Variant names:

• chr15-59737814-C-T
• rs4620904

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 0.141 in 152,050 control chromosomes in the GnomAD database, including 1,901 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 0.14 (1901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 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: 0.142 AC: 21502 AN: 151934 Hom.: 1900 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.141 AC: 21497 AN: 152050 Hom.: 1901 Cov.: 32 AF XY: 0.144 AC XY: 10724 AN XY: 74302

African (AFR) AF: 0.0337 AC: 1399 AN: 41522

American (AMR) AF: 0.160 AC: 2446 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5166

South Asian (SAS) AF: 0.206 AC: 994 AN: 4818

European-Finnish (FIN) AF: 0.198 AC: 2081 AN: 10530

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12369 AN: 67960

Other (OTH) AF: 0.170 AC: 360 AN: 2112

Alfa AF: 0.173 Hom.: 1316

Bravo AF: 0.132

Asia WGS AF: 0.193 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.51
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs4620904; hg19: chr15-60030013;