10-80034407-T-C

Variant names:

• chr10-80034407-T-C
• rs2342606
• ENST00000803265.1:n.104+410A>G

Variant summary

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

The ENST00000803265.1(ENSG00000304425):​n.104+410A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 150,550 control chromosomes in the GnomAD database, including 28,324 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 0.61 (28324 hom., cov: 28)
• Consequence: ENSG00000304425 ENST00000803265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930
• Publications: 6 publications found

Genes affected

ENSG00000304425 (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 (SAS) allele frequency at 95% confidence interval = 0.715 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
ENSG00000304425	ENST00000803265.1	n.104+410A>G		intron_variant	Intron 1 of 2
ENSG00000304425	ENST00000803266.1	n.94+410A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 91417 AN: 150442 Hom.: 28271 Cov.: 28

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.608 AC: 91525 AN: 150550 Hom.: 28324 Cov.: 28 AF XY: 0.608 AC XY: 44550 AN XY: 73316

African (AFR) AF: 0.700 AC: 28629 AN: 40914

American (AMR) AF: 0.557 AC: 8446 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2711 AN: 5088

South Asian (SAS) AF: 0.735 AC: 3524 AN: 4792

European-Finnish (FIN) AF: 0.560 AC: 5619 AN: 10028

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38623 AN: 67816

Other (OTH) AF: 0.601 AC: 1254 AN: 2088

Alfa AF: 0.577 Hom.: 82944

Bravo AF: 0.607

Asia WGS AF: 0.650 AC: 2260 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	3.4
DANN	Benign	0.26
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2342606; hg19: chr10-81794163;