chr18-62608007-C-T

Variant names:

• chr18-62608007-C-T
• rs10515988

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 0.134 in 152,122 control chromosomes in the GnomAD database, including 1,519 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 0.13 (1519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20418 AN: 152004 Hom.: 1522 Cov.: 32

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.134 AC: 20429 AN: 152122 Hom.: 1519 Cov.: 32 AF XY: 0.136 AC XY: 10079 AN XY: 74372

African (AFR) AF: 0.0743 AC: 3084 AN: 41518

American (AMR) AF: 0.170 AC: 2595 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 595 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5172

South Asian (SAS) AF: 0.212 AC: 1022 AN: 4812

European-Finnish (FIN) AF: 0.135 AC: 1431 AN: 10574

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10106 AN: 67982

Other (OTH) AF: 0.163 AC: 343 AN: 2110

Alfa AF: 0.148 Hom.: 1011

Bravo AF: 0.135

Asia WGS AF: 0.220 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.72
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10515988; hg19: chr18-60275240;