rs17875752

chr21-33324192-G-Tchr21-33324192-G-C

Variant summary

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

The ENST00000687762.2(ENSG00000289238):n.681C>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 0.38 in 151,646 control chromosomes in the GnomAD database, including 11,059 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 0.38 (11059 hom., cov: 32)
• Consequence: ENST00000687762.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687762.2	n.681C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57609 AN: 151528 Hom.: 11055 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.380 AC: 57628 AN: 151646 Hom.: 11059 Cov.: 32 AF XY: 0.379 AC XY: 28111 AN XY: 74122

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.403

Alfa AF: 0.388 Hom.: 1445

Bravo AF: 0.378

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.5
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17875752; hg19: chr21-34696497;