ENST00000444868.2:n.67+18444C>G

Variant names:

• chr21-16797178-G-C
• rs2824050
• ENST00000444868.2:n.67+18444C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444868.2(ENSG00000237735):​n.67+18444C>G variant causes a intron 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: ENSG00000237735 ENST00000444868.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 3 publications found

Genes affected

ENSG00000237735 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237735	ENST00000444868.2	n.67+18444C>G		intron_variant	Intron 1 of 2	3
ENSG00000304324	ENST00000802558.1	n.150+2003G>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.165 AC: 6822 AN: 41462

American (AMR) AF: 0.281 AC: 4270 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1283 AN: 5124

South Asian (SAS) AF: 0.241 AC: 1160 AN: 4812

European-Finnish (FIN) AF: 0.383 AC: 4050 AN: 10568

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23216 AN: 67856

Other (OTH) AF: 0.287 AC: 606 AN: 2108

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2824050; hg19: chr21-18169497;