chr15-60418070-T-G

Variant names:

• chr15-60418070-T-G
• rs10459628

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 0.653 in 152,082 control chromosomes in the GnomAD database, including 33,998 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 0.65 (33998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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: 0.653 AC: 99209 AN: 151962 Hom.: 33969 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.653 AC: 99293 AN: 152082 Hom.: 33998 Cov.: 32 AF XY: 0.663 AC XY: 49258 AN XY: 74324

African (AFR) AF: 0.443 AC: 18358 AN: 41448

American (AMR) AF: 0.696 AC: 10643 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2400 AN: 3470

East Asian (EAS) AF: 0.932 AC: 4823 AN: 5174

South Asian (SAS) AF: 0.828 AC: 3991 AN: 4818

European-Finnish (FIN) AF: 0.809 AC: 8545 AN: 10566

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.710 AC: 48301 AN: 68004

Other (OTH) AF: 0.648 AC: 1370 AN: 2114

Alfa AF: 0.683 Hom.: 61345

Bravo AF: 0.634

Asia WGS AF: 0.850 AC: 2956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.87
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs10459628; hg19: chr15-60710269;