21-36689322-C-A

Variant names:

• chr21-36689322-C-A
• rs1012959
• ENST00000832352.1:n.108+9587G>T

Variant summary

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

The ENST00000832352.1(ENSG00000231324):​n.108+9587G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,086 control chromosomes in the GnomAD database, including 12,670 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 0.39 (12670 hom., cov: 33)
• Consequence: ENSG00000231324 ENST00000832352.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 6 publications found

Genes affected

ENSG00000231324 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369308	NR_188245.1	n.83+9587G>T		intron_variant	Intron 1 of 2
LOC105369308	NR_188246.1	n.83+9587G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231324	ENST00000832352.1	n.108+9587G>T		intron_variant	Intron 1 of 2
ENSG00000231324	ENST00000832353.1	n.84+9587G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59891 AN: 151968 Hom.: 12669 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.394 AC: 59911 AN: 152086 Hom.: 12670 Cov.: 33 AF XY: 0.396 AC XY: 29424 AN XY: 74322

African (AFR) AF: 0.258 AC: 10688 AN: 41468

American (AMR) AF: 0.444 AC: 6787 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1393 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1354 AN: 5176

South Asian (SAS) AF: 0.278 AC: 1340 AN: 4816

European-Finnish (FIN) AF: 0.549 AC: 5805 AN: 10570

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31127 AN: 67984

Other (OTH) AF: 0.385 AC: 813 AN: 2114

Alfa AF: 0.423 Hom.: 29269

Bravo AF: 0.385

Asia WGS AF: 0.247 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1012959; hg19: chr21-38061622;