18-931660-T-C

Variant names:

• chr18-931660-T-C
• rs1557299

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 0.535 in 152,042 control chromosomes in the GnomAD database, including 22,300 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 0.54 (22300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.597 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: 0.535 AC: 81269 AN: 151922 Hom.: 22265 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.535 AC: 81361 AN: 152042 Hom.: 22300 Cov.: 32 AF XY: 0.534 AC XY: 39655 AN XY: 74300

African (AFR) AF: 0.415 AC: 17223 AN: 41456

American (AMR) AF: 0.607 AC: 9286 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1810 AN: 3464

East Asian (EAS) AF: 0.520 AC: 2684 AN: 5158

South Asian (SAS) AF: 0.496 AC: 2387 AN: 4816

European-Finnish (FIN) AF: 0.587 AC: 6197 AN: 10562

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40179 AN: 67974

Other (OTH) AF: 0.531 AC: 1121 AN: 2112

Alfa AF: 0.562 Hom.: 9352

Bravo AF: 0.535

Asia WGS AF: 0.511 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1557299; hg19: chr18-931661;