rs2051974

Variant names:

• chr17-13018328-T-A
• rs2051974

Your query was ambiguous. Multiple possible variants found:

• chr17-13018328-T-A
• chr17-13018328-T-C
• chr17-13018328-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892
• Publications: 9 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).

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 Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 137678 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 70712

African (AFR) AF: 0.00 AC: 0 AN: 3464

American (AMR) AF: 0.00 AC: 0 AN: 4206

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4756

East Asian (EAS) AF: 0.00 AC: 0 AN: 9372

South Asian (SAS) AF: 0.00 AC: 0 AN: 14774

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7108

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 618

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 84462

Other (OTH) AF: 0.00 AC: 0 AN: 8918

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		-0.89
PromoterAI		-0.048	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2051974; hg19: chr17-12921645;