chr9-4744743-T-C

Variant names:

• chr9-4744743-T-C
• rs409801
• ENST00000655730.1:n.495+2508T>C

Variant summary

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

The ENST00000655730.1(ENSG00000287759):​n.495+2508T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,052 control chromosomes in the GnomAD database, including 13,712 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 0.38 (13712 hom., cov: 32)
• Consequence: ENSG00000287759 ENST00000655730.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 17 publications found

Genes affected

ENSG00000287759 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 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
ENSG00000287759	ENST00000655730.1	n.495+2508T>C		intron_variant	Intron 1 of 1
ENSG00000287759	ENST00000663238.1	n.404+2508T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58189 AN: 151934 Hom.: 13711 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.383 AC: 58192 AN: 152052 Hom.: 13712 Cov.: 32 AF XY: 0.387 AC XY: 28760 AN XY: 74336

African (AFR) AF: 0.107 AC: 4446 AN: 41468

American (AMR) AF: 0.379 AC: 5779 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.659 AC: 3398 AN: 5158

South Asian (SAS) AF: 0.391 AC: 1887 AN: 4824

European-Finnish (FIN) AF: 0.583 AC: 6165 AN: 10574

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33945 AN: 67972

Other (OTH) AF: 0.379 AC: 801 AN: 2116

Alfa AF: 0.442 Hom.: 33027

Bravo AF: 0.355

Asia WGS AF: 0.464 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs409801; hg19: chr9-4744743;