rs10040744

Variant names:

• chr5-178157767-T-A
• rs10040744
• ENST00000697324.1:n.216+2873T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000697324.1(ENSG00000289726):​n.216+2873T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,020 control chromosomes in the GnomAD database, including 276 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 0.051 (276 hom., cov: 31)
• Consequence: ENSG00000289726 ENST00000697324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

ENSG00000289726 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0956 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
ENSG00000289726	ENST00000697324.1	n.216+2873T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7700 AN: 151902 Hom.: 275 Cov.: 31

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00852

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0378

Gnomad OTH AF: 0.0499

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

GnomAD4 genome AF: 0.0507 AC: 7706 AN: 152020 Hom.: 276 Cov.: 31 AF XY: 0.0486 AC XY: 3609 AN XY: 74320

Gnomad4 AFR AF: 0.0981

Gnomad4 AMR AF: 0.0350

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.00832

Gnomad4 FIN AF: 0.0277

Gnomad4 NFE AF: 0.0378

Gnomad4 OTH AF: 0.0493

Alfa AF: 0.0495 Hom.: 33

Bravo AF: 0.0516

Asia WGS AF: 0.0100 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10040744; hg19: chr5-177584768;