18-60083782-T-C

Variant names:

• chr18-60083782-T-C
• rs12957347

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 0.287 in 151,958 control chromosomes in the GnomAD database, including 6,905 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 0.29 (6905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 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: 0.287 AC: 43588 AN: 151840 Hom.: 6898 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.287 AC: 43644 AN: 151958 Hom.: 6905 Cov.: 32 AF XY: 0.283 AC XY: 20990 AN XY: 74274

African (AFR) AF: 0.419 AC: 17383 AN: 41446

American (AMR) AF: 0.196 AC: 2987 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3466

East Asian (EAS) AF: 0.169 AC: 876 AN: 5186

South Asian (SAS) AF: 0.341 AC: 1638 AN: 4808

European-Finnish (FIN) AF: 0.174 AC: 1845 AN: 10574

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17056 AN: 67914

Other (OTH) AF: 0.287 AC: 606 AN: 2108

Alfa AF: 0.261 Hom.: 7486

Bravo AF: 0.293

Asia WGS AF: 0.226 AC: 786 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
DANN	Benign	0.57
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs12957347; hg19: chr18-57751014;