chr17-21276149-C-A

Position:

• chr17-21276149-C-A

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: ENST00000692381.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000692381.2	n.187C>A		non_coding_transcript_exon_variant	1/1

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;