rs2064040

chr21-15212021-G-Achr21-15212021-G-T

Variant summary

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

The ENST00000673983.1(ENSG00000288555):n.345+8171C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,816 control chromosomes in the GnomAD database, including 13,225 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 0.41 (13225 hom., cov: 31)
• Consequence: ENST00000673983.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 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
	ENST00000673983.1	n.345+8171C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62444 AN: 151696 Hom.: 13228 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.411 AC: 62453 AN: 151816 Hom.: 13225 Cov.: 31 AF XY: 0.407 AC XY: 30205 AN XY: 74196

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.396

Alfa AF: 0.460 Hom.: 27025

Bravo AF: 0.410

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.20
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2064040; hg19: chr21-16584341; COSMIC: COSV53453266;