rs2835704

Variant names:

• chr21-37358658-G-A
• rs2835704
• ENST00000663813.1:n.187+8014C>T

Variant summary

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

The ENST00000663813.1(ENSG00000287637):​n.187+8014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,092 control chromosomes in the GnomAD database, including 21,292 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 0.53 (21292 hom., cov: 33)
• Consequence: ENSG00000287637 ENST00000663813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663813.1. 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
	ENSG00000287637	ENST00000663813.1		n.187+8014C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80068 AN: 151972 Hom.: 21265 Cov.: 33

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.527 AC: 80144 AN: 152092 Hom.: 21292 Cov.: 33 AF XY: 0.524 AC XY: 38974 AN XY: 74326

African (AFR) AF: 0.560 AC: 23262 AN: 41506

American (AMR) AF: 0.493 AC: 7531 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2225 AN: 3472

East Asian (EAS) AF: 0.506 AC: 2615 AN: 5170

South Asian (SAS) AF: 0.603 AC: 2908 AN: 4826

European-Finnish (FIN) AF: 0.484 AC: 5110 AN: 10548

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34778 AN: 67976

Other (OTH) AF: 0.555 AC: 1169 AN: 2108

Alfa AF: 0.521 Hom.: 2722

Bravo AF: 0.528

Asia WGS AF: 0.561 AC: 1951 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	3.1
DANN	Benign	0.40
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2835704; hg19: chr21-38730960;