17-31545612-C-T

Variant names:

• chr17-31545612-C-T
• rs2018971

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 0.532 in 151,770 control chromosomes in the GnomAD database, including 22,089 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 0.53 (22089 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 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: 0.532 AC: 80726 AN: 151652 Hom.: 22079 Cov.: 31

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.532 AC: 80765 AN: 151770 Hom.: 22089 Cov.: 31 AF XY: 0.531 AC XY: 39369 AN XY: 74186

African (AFR) AF: 0.399 AC: 16471 AN: 41318

American (AMR) AF: 0.496 AC: 7564 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2094 AN: 3470

East Asian (EAS) AF: 0.710 AC: 3677 AN: 5176

South Asian (SAS) AF: 0.550 AC: 2653 AN: 4826

European-Finnish (FIN) AF: 0.601 AC: 6314 AN: 10514

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40120 AN: 67922

Other (OTH) AF: 0.551 AC: 1158 AN: 2100

Alfa AF: 0.568 Hom.: 3303

Bravo AF: 0.520

Asia WGS AF: 0.591 AC: 2054 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.43
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2018971; hg19: chr17-29872631;