rs2835704

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287637 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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.187+8014C>T		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.555

Alfa AF: 0.520 Hom.: 2600

Bravo AF: 0.528

Asia WGS AF: 0.561 AC: 1951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2835704; hg19: chr21-38730960;