10-43074205-A-G

Variant names:

• chr10-43074205-A-G
• rs2505995
• ENST00000794440.1:n.52-2694T>C

Variant summary

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

The ENST00000794440.1(ENSG00000303432):​n.52-2694T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,952 control chromosomes in the GnomAD database, including 13,989 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 0.43 (13989 hom., cov: 33)
• Consequence: ENSG00000303432 ENST00000794440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.474 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
ENSG00000303432	ENST00000794440.1	n.52-2694T>C		intron_variant	Intron 1 of 2
ENSG00000303432	ENST00000794441.1	n.117-2694T>C		intron_variant	Intron 1 of 3
ENSG00000303432	ENST00000794442.1	n.108-2694T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64701 AN: 151832 Hom.: 13960 Cov.: 33

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.426 AC: 64781 AN: 151952 Hom.: 13989 Cov.: 33 AF XY: 0.426 AC XY: 31609 AN XY: 74244

African (AFR) AF: 0.480 AC: 19866 AN: 41426

American (AMR) AF: 0.454 AC: 6927 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1644 AN: 5170

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4818

European-Finnish (FIN) AF: 0.370 AC: 3893 AN: 10532

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.409 AC: 27814 AN: 67970

Other (OTH) AF: 0.418 AC: 882 AN: 2110

Alfa AF: 0.416 Hom.: 5321

Bravo AF: 0.436

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.26
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2505995; hg19: chr10-43569653;