rs17231506

Variant names:

• chr16-56960616-C-G
• rs17231506

Your query was ambiguous. Multiple possible variants found:

• chr16-56960616-C-G
• chr16-56960616-C-T

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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 78 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=-0.91).

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.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 328178 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 187218

African (AFR) AF: 0.00 AC: 0 AN: 9598

American (AMR) AF: 0.00 AC: 0 AN: 30056

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11056

East Asian (EAS) AF: 0.00 AC: 0 AN: 11258

South Asian (SAS) AF: 0.00 AC: 0 AN: 61346

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 14334

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2810

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 172500

Other (OTH) AF: 0.00 AC: 0 AN: 15220

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 10081

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.58
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs17231506; hg19: chr16-56994528;