18-60120327-T-C

Variant names:

• chr18-60120327-T-C
• rs1893512

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 0.416 in 151,776 control chromosomes in the GnomAD database, including 15,383 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 0.42 (15383 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 8 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 = 0.675 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: 0.416 AC: 63034 AN: 151658 Hom.: 15354 Cov.: 31

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.416 AC: 63119 AN: 151776 Hom.: 15383 Cov.: 31 AF XY: 0.408 AC XY: 30279 AN XY: 74164

African (AFR) AF: 0.681 AC: 28171 AN: 41346

American (AMR) AF: 0.313 AC: 4771 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3468

East Asian (EAS) AF: 0.186 AC: 960 AN: 5150

South Asian (SAS) AF: 0.416 AC: 1998 AN: 4806

European-Finnish (FIN) AF: 0.265 AC: 2797 AN: 10556

Middle Eastern (MID) AF: 0.390 AC: 113 AN: 290

European-Non Finnish (NFE) AF: 0.329 AC: 22313 AN: 67900

Other (OTH) AF: 0.384 AC: 810 AN: 2110

Alfa AF: 0.358 Hom.: 18104

Bravo AF: 0.429

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1893512; hg19: chr18-57787559;