10-43074362-C-T

Variant names:

• chr10-43074362-C-T
• rs2505996
• ENST00000794440.1:n.51+2699G>A

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.51+2699G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,294 control chromosomes in the GnomAD database, including 9,570 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 0.35 (9570 hom., cov: 31)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 0 publications found

Genes affected

ENSG00000303432 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794440.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303432	ENST00000794440.1		n.51+2699G>A		intron	N/A
	ENSG00000303432	ENST00000794441.1		n.116+2671G>A		intron	N/A
	ENSG00000303432	ENST00000794442.1		n.107+2671G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52582 AN: 151180 Hom.: 9548 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.348 AC: 52629 AN: 151294 Hom.: 9570 Cov.: 31 AF XY: 0.349 AC XY: 25810 AN XY: 73890

African (AFR) AF: 0.245 AC: 10075 AN: 41160

American (AMR) AF: 0.406 AC: 6168 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3464

East Asian (EAS) AF: 0.317 AC: 1629 AN: 5132

South Asian (SAS) AF: 0.416 AC: 1982 AN: 4768

European-Finnish (FIN) AF: 0.364 AC: 3793 AN: 10428

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26544 AN: 67834

Other (OTH) AF: 0.354 AC: 742 AN: 2098

Alfa AF: 0.345 Hom.: 1159

Bravo AF: 0.346

Asia WGS AF: 0.353 AC: 1223 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.99
DANN	Benign	0.45
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2505996; hg19: chr10-43569810;