rs762372

Variant names:

• chr21-37045061-G-A
• rs762372
• ENST00000787370.1:n.178+1759C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-37045061-G-A
• chr21-37045061-G-C
• chr21-37045061-G-T

Variant summary

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

The ENST00000787370.1(ENSG00000302499):​n.178+1759C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,276 control chromosomes in the GnomAD database, including 20,332 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 0.51 (20332 hom., cov: 29)
• Consequence: ENSG00000302499 ENST00000787370.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 1 publications found

Genes affected

ENSG00000302499 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302499	ENST00000787370.1	n.178+1759C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.515 AC: 77850 AN: 151160 Hom.: 20336 Cov.: 29

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.515 AC: 77878 AN: 151276 Hom.: 20332 Cov.: 29 AF XY: 0.518 AC XY: 38229 AN XY: 73846

African (AFR) AF: 0.445 AC: 18334 AN: 41200

American (AMR) AF: 0.538 AC: 8183 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1482 AN: 3466

East Asian (EAS) AF: 0.396 AC: 2041 AN: 5148

South Asian (SAS) AF: 0.616 AC: 2955 AN: 4800

European-Finnish (FIN) AF: 0.550 AC: 5681 AN: 10326

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37561 AN: 67824

Other (OTH) AF: 0.494 AC: 1039 AN: 2104

Alfa AF: 0.527 Hom.: 3175

Bravo AF: 0.508

Asia WGS AF: 0.516 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs762372; hg19: chr21-38417361;