21-15440233-C-A

Variant names:

• chr21-15440233-C-A
• rs1736020
• ENST00000634642.1:n.343+3791G>T

Variant summary

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

The ENST00000634642.1(ENSG00000229425):​n.343+3791G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,878 control chromosomes in the GnomAD database, including 9,537 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 0.33 (9537 hom., cov: 31)
• Consequence: ENSG00000229425 ENST00000634642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 45 publications found

Genes affected

ENSG00000229425 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634642.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927745	NR_188234.1		n.341+3791G>T		intron	N/A
	LOC101927745	NR_188235.1		n.341+3791G>T		intron	N/A
	LOC101927745	NR_188236.1		n.341+3791G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229425	ENST00000634642.1	TSL:3	n.343+3791G>T		intron	N/A
	ENSG00000229425	ENST00000634644.1	TSL:5	n.952+27055G>T		intron	N/A
	ENSG00000229425	ENST00000634659.1	TSL:5	n.307+993G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49814 AN: 151760 Hom.: 9532 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.328 AC: 49828 AN: 151878 Hom.: 9537 Cov.: 31 AF XY: 0.324 AC XY: 24083 AN XY: 74228

African (AFR) AF: 0.132 AC: 5459 AN: 41450

American (AMR) AF: 0.387 AC: 5898 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1076 AN: 3460

East Asian (EAS) AF: 0.186 AC: 957 AN: 5156

South Asian (SAS) AF: 0.365 AC: 1757 AN: 4808

European-Finnish (FIN) AF: 0.389 AC: 4085 AN: 10514

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29185 AN: 67920

Other (OTH) AF: 0.361 AC: 762 AN: 2112

Alfa AF: 0.396 Hom.: 35526

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.7
DANN	Benign	0.65
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1736020; hg19: chr21-16812552;