ENST00000635525.2:n.3612C>A

Variant names:

• chr21-15523514-G-T
• rs2823324
• ENST00000635525.2:n.3612C>A

Variant summary

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

The ENST00000635525.2(ENSG00000229425):​n.3612C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,160 control chromosomes in the GnomAD database, including 3,218 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 0.13 (3217 hom., cov: 32)
  • Exomes 𝑓: 0.031 (1 hom.)
• Consequence: ENSG00000229425 ENST00000635525.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635525.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229425	ENST00000635525.2	TSL:5	n.3612C>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000229425	ENST00000657904.1		n.1650C>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000229425	ENST00000669763.2		n.3731C>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19703 AN: 151944 Hom.: 3197 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.00650

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0189

Gnomad OTH AF: 0.101

GnomAD4 exome AF: 0.0306 AC: 3 AN: 98 Hom.: 1 Cov.: 0 AF XY: 0.0256 AC XY: 2 AN XY: 78

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0233 AC: 2 AN: 86

Other (OTH) AF: 0.125 AC: 1 AN: 8

GnomAD4 genome AF: 0.130 AC: 19780 AN: 152062 Hom.: 3217 Cov.: 32 AF XY: 0.127 AC XY: 9443 AN XY: 74362

African (AFR) AF: 0.383 AC: 15843 AN: 41388

American (AMR) AF: 0.0761 AC: 1164 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3468

East Asian (EAS) AF: 0.140 AC: 726 AN: 5170

South Asian (SAS) AF: 0.0681 AC: 328 AN: 4818

European-Finnish (FIN) AF: 0.00650 AC: 69 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0189 AC: 1285 AN: 67998

Other (OTH) AF: 0.100 AC: 211 AN: 2106

Alfa AF: 0.0479 Hom.: 1382

Bravo AF: 0.147

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.28
PhyloP100		-0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2823324;

hg19: chr21-16895833;