rs10940434

Variant names:

• chr5-54879078-T-C
• rs10940434
• ENST00000736670.1:n.372-12034A>G

Variant summary

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

The ENST00000736670.1(ENSG00000296132):​n.372-12034A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,928 control chromosomes in the GnomAD database, including 21,069 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 0.49 (21069 hom., cov: 31)
• Consequence: ENSG00000296132 ENST00000736670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 5 publications found

Genes affected

ENSG00000296132 (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 (AMR) allele frequency at 95% confidence interval = 0.613 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
ENSG00000296132	ENST00000736670.1	n.372-12034A>G		intron_variant	Intron 1 of 1
ENSG00000296132	ENST00000736672.1	n.229-12034A>G		intron_variant	Intron 1 of 1
ENSG00000296132	ENST00000736673.1	n.144-10416A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74863 AN: 151810 Hom.: 21063 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.493 AC: 74880 AN: 151928 Hom.: 21069 Cov.: 31 AF XY: 0.498 AC XY: 36992 AN XY: 74260

African (AFR) AF: 0.213 AC: 8811 AN: 41404

American (AMR) AF: 0.624 AC: 9525 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1654 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3185 AN: 5172

South Asian (SAS) AF: 0.474 AC: 2283 AN: 4818

European-Finnish (FIN) AF: 0.643 AC: 6770 AN: 10536

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40975 AN: 67942

Other (OTH) AF: 0.495 AC: 1045 AN: 2110

Alfa AF: 0.565 Hom.: 96135

Bravo AF: 0.483

Asia WGS AF: 0.496 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.42
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10940434; hg19: chr5-54174906;