10-43070912-A-G

Variant names:

• chr10-43070912-A-G
• rs2505991
• ENST00000794445.1:n.568T>C

Variant summary

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

The ENST00000794445.1(ENSG00000303432):​n.568T>C 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 0.8 in 152,236 control chromosomes in the GnomAD database, including 49,748 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 0.80 (49748 hom., cov: 35)
• Consequence: ENSG00000303432 ENST00000794445.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 1 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 = 0.945 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	ENST00000794445.1	n.568T>C		non_coding_transcript_exon_variant	Exon 3 of 5
ENSG00000303432	ENST00000794449.1	n.578T>C		non_coding_transcript_exon_variant	Exon 3 of 5
ENSG00000303432	ENST00000794462.1	n.540T>C		non_coding_transcript_exon_variant	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121688 AN: 152118 Hom.: 49682 Cov.: 35

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.800 AC: 121822 AN: 152236 Hom.: 49748 Cov.: 35 AF XY: 0.792 AC XY: 58906 AN XY: 74400

African (AFR) AF: 0.953 AC: 39642 AN: 41586

American (AMR) AF: 0.770 AC: 11780 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3472

East Asian (EAS) AF: 0.534 AC: 2748 AN: 5142

South Asian (SAS) AF: 0.720 AC: 3468 AN: 4818

European-Finnish (FIN) AF: 0.647 AC: 6861 AN: 10600

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52261 AN: 67998

Other (OTH) AF: 0.784 AC: 1658 AN: 2116

Alfa AF: 0.700 Hom.: 2286

Bravo AF: 0.818

Asia WGS AF: 0.663 AC: 2306 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	3.7
DANN	Benign	0.76
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2505991; hg19: chr10-43566360;