rs2835699

Positions:

• chr21-37349007-T-G
• chr21-37349007-T-C

Variant summary

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

The ENST00000663813.1(ENSG00000287637):​n.188-9553A>C variant causes a intron, non coding transcript 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: ENST00000663813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663813.1	n.188-9553A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.441

Alfa AF: 0.373 Hom.: 21592

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2835699; hg19: chr21-38721309;