chr18-931660-T-C

Variant names:

• chr18-931660-T-C
• rs1557299

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.531

Alfa AF: 0.566 Hom.: 6046

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1557299; hg19: chr18-931661;