21-37349007-T-G

Variant names:

• chr21-37349007-T-G
• rs2835699
• ENST00000663813.1:n.188-9553A>C

Variant summary

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

The ENST00000663813.1(ENSG00000287637):​n.188-9553A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,992 control chromosomes in the GnomAD database, including 12,812 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 (12812 hom., cov: 32)
• Consequence: ENSG00000287637 ENST00000663813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 3 publications found

Genes affected

ENSG00000287637 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 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
ENSG00000287637	ENST00000663813.1	n.188-9553A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61488 AN: 151874 Hom.: 12790 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.405 AC: 61558 AN: 151992 Hom.: 12812 Cov.: 32 AF XY: 0.403 AC XY: 29968 AN XY: 74306

African (AFR) AF: 0.495 AC: 20535 AN: 41486

American (AMR) AF: 0.367 AC: 5605 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3470

East Asian (EAS) AF: 0.436 AC: 2252 AN: 5162

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4818

European-Finnish (FIN) AF: 0.326 AC: 3437 AN: 10536

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24441 AN: 67928

Other (OTH) AF: 0.441 AC: 932 AN: 2112

Alfa AF: 0.381 Hom.: 35065

Bravo AF: 0.412

Asia WGS AF: 0.480 AC: 1668 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.4
DANN	Benign	0.90
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2835699; hg19: chr21-38721309;