21-36634021-G-A

Variant names:

• chr21-36634021-G-A
• rs2051396
• ENST00000457669.1:n.244-451C>T

Variant summary

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

The ENST00000457669.1(ENSG00000231324):​n.244-451C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,152 control chromosomes in the GnomAD database, including 5,017 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 0.26 (5017 hom., cov: 32)
• Consequence: ENSG00000231324 ENST00000457669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

Genes affected

ENSG00000231324 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369308	NR_188245.1	n.1102-451C>T		intron_variant	Intron 2 of 2
LOC105369308	NR_188246.1	n.6300-451C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231324	ENST00000457669.1	n.244-451C>T		intron_variant	Intron 1 of 1	3
ENSG00000231324	ENST00000832352.1	n.1127-451C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38886 AN: 152034 Hom.: 5016 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.256 AC: 38895 AN: 152152 Hom.: 5017 Cov.: 32 AF XY: 0.255 AC XY: 18965 AN XY: 74392

African (AFR) AF: 0.247 AC: 10235 AN: 41502

American (AMR) AF: 0.197 AC: 3013 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 710 AN: 3472

East Asian (EAS) AF: 0.177 AC: 915 AN: 5184

South Asian (SAS) AF: 0.318 AC: 1533 AN: 4818

European-Finnish (FIN) AF: 0.279 AC: 2951 AN: 10590

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18730 AN: 67978

Other (OTH) AF: 0.231 AC: 488 AN: 2110

Alfa AF: 0.150 Hom.: 296

Bravo AF: 0.244

Asia WGS AF: 0.255 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.049
DANN	Benign	0.71
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2051396; hg19: chr21-38006319;