10-43068406-T-C

Variant names:

• chr10-43068406-T-C
• rs3026720
• ENST00000794447.1:n.332A>G

Variant summary

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

The ENST00000794447.1(ENSG00000303432):​n.332A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,164 control chromosomes in the GnomAD database, including 8,094 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 0.28 (8094 hom., cov: 33)
• Consequence: ENSG00000303432 ENST00000794447.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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	ENST00000794447.1	n.332A>G		non_coding_transcript_exon_variant	Exon 3 of 5
ENSG00000303432	ENST00000794448.1	n.362A>G		non_coding_transcript_exon_variant	Exon 3 of 5
ENSG00000303432	ENST00000794454.1	n.323A>G		non_coding_transcript_exon_variant	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43273 AN: 152046 Hom.: 8076 Cov.: 33

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.285 AC: 43334 AN: 152164 Hom.: 8094 Cov.: 33 AF XY: 0.277 AC XY: 20579 AN XY: 74392

African (AFR) AF: 0.530 AC: 21969 AN: 41480

American (AMR) AF: 0.249 AC: 3804 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3470

East Asian (EAS) AF: 0.123 AC: 638 AN: 5180

South Asian (SAS) AF: 0.0924 AC: 446 AN: 4828

European-Finnish (FIN) AF: 0.116 AC: 1235 AN: 10602

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13637 AN: 67994

Other (OTH) AF: 0.279 AC: 589 AN: 2110

Alfa AF: 0.224 Hom.: 16721

Bravo AF: 0.308

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3026720; hg19: chr10-43563854;