rs10040744

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000289726 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697324.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289726	ENST00000697324.1		n.216+2873T>A		intron	N/A

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

African (AFR) AF: 0.0981 AC: 4066 AN: 41456

American (AMR) AF: 0.0350 AC: 535 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 47 AN: 3468

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5140

South Asian (SAS) AF: 0.00832 AC: 40 AN: 4810

European-Finnish (FIN) AF: 0.0277 AC: 293 AN: 10590

Middle Eastern (MID) AF: 0.0621 AC: 18 AN: 290

European-Non Finnish (NFE) AF: 0.0378 AC: 2568 AN: 67974

Other (OTH) AF: 0.0493 AC: 104 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.52
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10040744; hg19: chr5-177584768;