rs2824050

Positions:

• chr21-16797178-G-C
• chr21-16797178-G-T

Variant summary

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

The ENST00000444868.2(ENSG00000237735):​n.67+18444C>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 0.282 in 151,812 control chromosomes in the GnomAD database, including 6,531 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 0.28 (6531 hom., cov: 32)
• Consequence: ENST00000444868.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000444868.2	n.67+18444C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42757 AN: 151692 Hom.: 6524 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.282 AC: 42775 AN: 151812 Hom.: 6531 Cov.: 32 AF XY: 0.282 AC XY: 20889 AN XY: 74168

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.287

Alfa AF: 0.204 Hom.: 490

Bravo AF: 0.269

Asia WGS AF: 0.238 AC: 825 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
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: rs2824050; hg19: chr21-18169497;