13-39128618-A-G

Variant names:

• chr13-39128618-A-G
• rs1413042
• ENST00000614005.1:n.258-62985A>G

Variant summary

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

The ENST00000614005.1(ENSG00000273507):​n.258-62985A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,168 control chromosomes in the GnomAD database, including 4,275 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 0.23 (4275 hom., cov: 32)
• Consequence: ENSG00000273507 ENST00000614005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427
• Publications: 2 publications found

Genes affected

ENSG00000273507 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 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
ENSG00000273507	ENST00000614005.1	n.258-62985A>G		intron_variant	Intron 1 of 2	3
ENSG00000273507	ENST00000655342.1	n.257-62985A>G		intron_variant	Intron 1 of 2
ENSG00000273507	ENST00000668183.1	n.258-40773A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34248 AN: 152050 Hom.: 4269 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.225 AC: 34284 AN: 152168 Hom.: 4275 Cov.: 32 AF XY: 0.228 AC XY: 16976 AN XY: 74390

African (AFR) AF: 0.308 AC: 12794 AN: 41490

American (AMR) AF: 0.191 AC: 2922 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3466

East Asian (EAS) AF: 0.476 AC: 2459 AN: 5170

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4822

European-Finnish (FIN) AF: 0.206 AC: 2181 AN: 10602

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11172 AN: 67996

Other (OTH) AF: 0.216 AC: 457 AN: 2116

Alfa AF: 0.113 Hom.: 164

Bravo AF: 0.230

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.91
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1413042; hg19: chr13-39702755;