ENST00000744989.1:n.48+14637G>C

Variant names:

• chr13-37611674-G-C
• rs9547977
• ENST00000744989.1:n.48+14637G>C

Variant summary

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

The ENST00000744989.1(ENSG00000297050):​n.48+14637G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,264 control chromosomes in the GnomAD database, including 3,721 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 0.20 (3721 hom., cov: 31)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 2 publications found

Genes affected

ENSG00000297050 (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 (NFE) allele frequency at 95% confidence interval = 0.272 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
ENSG00000297050	ENST00000744989.1	n.48+14637G>C		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1	n.70+14637G>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30495 AN: 151144 Hom.: 3722 Cov.: 31

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0631

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.202 AC: 30497 AN: 151264 Hom.: 3721 Cov.: 31 AF XY: 0.202 AC XY: 14893 AN XY: 73856

African (AFR) AF: 0.0784 AC: 3231 AN: 41236

American (AMR) AF: 0.170 AC: 2580 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3462

East Asian (EAS) AF: 0.0634 AC: 324 AN: 5110

South Asian (SAS) AF: 0.139 AC: 665 AN: 4798

European-Finnish (FIN) AF: 0.338 AC: 3491 AN: 10326

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.276 AC: 18705 AN: 67838

Other (OTH) AF: 0.203 AC: 426 AN: 2100

Alfa AF: 0.130 Hom.: 270

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.38
DANN	Benign	0.40
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs9547977; hg19: chr13-38185811;