rs2001651

Variant names:

• chr17-21276149-C-A
• rs2001651
• ENST00000692381.2:n.187C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-21276149-C-A
• chr17-21276149-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000692381.2(ENSG00000289453):​n.187C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,084 control chromosomes in the GnomAD database, including 32,739 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 0.65 (32739 hom., cov: 34)
• Consequence: ENSG00000289453 ENST00000692381.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

Genes affected

ENSG00000289453 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 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
ENSG00000289453	ENST00000692381.2	n.187C>A		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99453 AN: 151966 Hom.: 32719 Cov.: 34

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.654 AC: 99518 AN: 152084 Hom.: 32739 Cov.: 34 AF XY: 0.655 AC XY: 48667 AN XY: 74350

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.643

Alfa AF: 0.644 Hom.: 36444

Bravo AF: 0.642

Asia WGS AF: 0.637 AC: 2217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001651; hg19: chr17-21179461; COSMIC: COSV60076842;