ENST00000624379.1:n.3624G>A

Variant names:

• chr13-37143095-C-T
• rs10507445
• ENST00000624379.1:n.3624G>A

Variant summary

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

The ENST00000624379.1(ENSG00000279511):​n.3624G>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 0.0245 in 152,276 control chromosomes in the GnomAD database, including 56 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 0.025 (56 hom., cov: 32)
  • Exomes 𝑓: 0.016 (0 hom.)
• Consequence: ENSG00000279511 ENST00000624379.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 3 publications found

Genes affected

ENSG00000279511 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0504 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
ENSG00000279511	ENST00000624379.1	n.3624G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000307674	ENST00000827784.1	n.352+36784C>T		intron_variant	Intron 3 of 4
ENSG00000307674	ENST00000827785.1	n.195+38359C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0245 AC: 3721 AN: 152094 Hom.: 56 Cov.: 32

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.0249

GnomAD4 exome AF: 0.0156 AC: 1 AN: 64 Hom.: 0 Cov.: 0 AF XY: 0.0333 AC XY: 1 AN XY: 30

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0167 AC: 1 AN: 60

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0245 AC: 3735 AN: 152212 Hom.: 56 Cov.: 32 AF XY: 0.0251 AC XY: 1867 AN XY: 74414

African (AFR) AF: 0.0522 AC: 2170 AN: 41542

American (AMR) AF: 0.0145 AC: 221 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 64 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.00435 AC: 21 AN: 4828

European-Finnish (FIN) AF: 0.0202 AC: 214 AN: 10594

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0142 AC: 969 AN: 68018

Other (OTH) AF: 0.0246 AC: 52 AN: 2110

Alfa AF: 0.0189 Hom.: 54

Bravo AF: 0.0251

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.67
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs10507445; hg19: chr13-37717232;