rs2931024

Variant names:

• chr18-78742001-T-C
• rs2931024

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 0.247 in 152,246 control chromosomes in the GnomAD database, including 5,126 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 0.25 (5126 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 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: 0.247 AC: 37617 AN: 152128 Hom.: 5118 Cov.: 34

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.247 AC: 37664 AN: 152246 Hom.: 5126 Cov.: 34 AF XY: 0.245 AC XY: 18247 AN XY: 74438

African (AFR) AF: 0.339 AC: 14090 AN: 41538

American (AMR) AF: 0.270 AC: 4128 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3472

East Asian (EAS) AF: 0.0419 AC: 217 AN: 5184

South Asian (SAS) AF: 0.0932 AC: 450 AN: 4826

European-Finnish (FIN) AF: 0.232 AC: 2460 AN: 10604

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15063 AN: 68004

Other (OTH) AF: 0.248 AC: 524 AN: 2112

Alfa AF: 0.223 Hom.: 16774

Bravo AF: 0.253

Asia WGS AF: 0.0960 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.45
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs2931024; hg19: chr18-76502001;