rs2835702

Variant names:

• chr21-37352009-T-C
• rs2835702
• ENST00000663813.1:n.188-12555A>G

Your query was ambiguous. Multiple possible variants found:

• chr21-37352009-T-C
• chr21-37352009-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663813.1(ENSG00000287637):​n.188-12555A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,170 control chromosomes in the GnomAD database, including 2,693 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 0.18 (2693 hom., cov: 32)
• Consequence: ENSG00000287637 ENST00000663813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

Genes affected

ENSG00000287637 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 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.188-12555A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26947 AN: 152052 Hom.: 2683 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.177 AC: 26984 AN: 152170 Hom.: 2693 Cov.: 32 AF XY: 0.181 AC XY: 13501 AN XY: 74412

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.192

Alfa AF: 0.164 Hom.: 586

Bravo AF: 0.180

Asia WGS AF: 0.357 AC: 1240 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.5
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2835702; hg19: chr21-38724311;