rs2064040

Variant names:

• chr21-15212021-G-A
• rs2064040
• ENST00000673983.1:n.345+8171C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-15212021-G-A
• chr21-15212021-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673983.1(ENSG00000288555):​n.345+8171C>T variant causes a intron 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: ENSG00000288555 ENST00000673983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 4 publications found

Genes affected

ENSG00000288555 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673983.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288555	ENST00000673983.1		n.345+8171C>T		intron	N/A

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

African (AFR) AF: 0.296 AC: 12233 AN: 41392

American (AMR) AF: 0.434 AC: 6619 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1643 AN: 3466

East Asian (EAS) AF: 0.430 AC: 2221 AN: 5166

South Asian (SAS) AF: 0.417 AC: 2005 AN: 4804

European-Finnish (FIN) AF: 0.424 AC: 4452 AN: 10494

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31781 AN: 67936

Other (OTH) AF: 0.396 AC: 833 AN: 2104

Alfa AF: 0.452 Hom.: 61045

Bravo AF: 0.410

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.20
DANN	Benign	0.52
PhyloP100		-0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2064040;

hg19: chr21-16584341;

COSMIC: COSV53453266;