15-30003661-G-T

Variant names:

• chr15-30003661-G-T
• rs6492918

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 0.601 in 151,898 control chromosomes in the GnomAD database, including 28,159 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 0.60 (28159 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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: 0.601 AC: 91228 AN: 151780 Hom.: 28139 Cov.: 31

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.601 AC: 91279 AN: 151898 Hom.: 28159 Cov.: 31 AF XY: 0.606 AC XY: 44980 AN XY: 74226

African (AFR) AF: 0.480 AC: 19870 AN: 41406

American (AMR) AF: 0.605 AC: 9243 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1993 AN: 3466

East Asian (EAS) AF: 0.930 AC: 4786 AN: 5144

South Asian (SAS) AF: 0.598 AC: 2873 AN: 4804

European-Finnish (FIN) AF: 0.648 AC: 6826 AN: 10542

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43640 AN: 67962

Other (OTH) AF: 0.635 AC: 1337 AN: 2104

Alfa AF: 0.635 Hom.: 44952

Bravo AF: 0.600

Asia WGS AF: 0.722 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.57
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6492918; hg19: chr15-30295864;