21-37982733-T-C

Position:

• chr21-37982733-T-C

Variant summary

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

The ENST00000398948.5(DSCR4):​n.315-29728A>G 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 0.377 in 151,982 control chromosomes in the GnomAD database, including 11,297 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 0.38 (11297 hom., cov: 31)
• Consequence: DSCR4 ENST00000398948.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

Genes affected

DSCR4 (HGNC:3045): (Down syndrome critical region 4) The gene is found in a region of chromosome 21 that has been linked to the pathogenesis of Down syndrome. This gene is transcribed from a bi-directional promoter located in an endogenous retrovirus. [provided by RefSeq, Jan 2015]

KCNJ6 (HGNC:6267): (potassium inwardly rectifying channel subfamily J member 6) This gene encodes a member of the G protein-coupled inwardly-rectifying potassium channel family of inward rectifier potassium channels. This type of potassium channel allows a greater flow of potassium into the cell than out of it. These proteins modulate many physiological processes, including heart rate in cardiac cells and circuit activity in neuronal cells, through G-protein coupled receptor stimulation. Mutations in this gene are associated with Keppen-Lubinsky Syndrome, a rare condition characterized by severe developmental delay, facial dysmorphism, and intellectual disability. [provided by RefSeq, Apr 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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
DSCR4	ENST00000398948.5	n.315-29728A>G		intron_variant, non_coding_transcript_variant		5
KCNJ6	ENST00000645093.1	c.-28+137574A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57206 AN: 151864 Hom.: 11275 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.377 AC: 57272 AN: 151982 Hom.: 11297 Cov.: 31 AF XY: 0.378 AC XY: 28118 AN XY: 74332

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.389

Alfa AF: 0.373 Hom.: 22142

Bravo AF: 0.385

Asia WGS AF: 0.608 AC: 2106 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836079; hg19: chr21-39355035;