chr10-46092487-G-A

Variant names:

• chr10-46092487-G-A
• rs7071471
• ENST00000809063.1:n.164G>A

Variant summary

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

The ENST00000809063.1(ENSG00000305148):​n.164G>A 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 0.473 in 152,008 control chromosomes in the GnomAD database, including 17,230 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 0.47 (17230 hom., cov: 32)
• Consequence: ENSG00000305148 ENST00000809063.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961
• Publications: 19 publications found

Genes affected

ENSG00000305148 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809063.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305148	ENST00000809063.1		n.164G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000305148	ENST00000809064.1		n.755G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000305148	ENST00000809061.1		n.336+545G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71778 AN: 151890 Hom.: 17196 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.473 AC: 71867 AN: 152008 Hom.: 17230 Cov.: 32 AF XY: 0.474 AC XY: 35239 AN XY: 74302

African (AFR) AF: 0.540 AC: 22376 AN: 41462

American (AMR) AF: 0.428 AC: 6547 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1882 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2330 AN: 5146

South Asian (SAS) AF: 0.595 AC: 2863 AN: 4810

European-Finnish (FIN) AF: 0.386 AC: 4084 AN: 10580

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30125 AN: 67946

Other (OTH) AF: 0.486 AC: 1026 AN: 2110

Alfa AF: 0.461 Hom.: 22804

Bravo AF: 0.472

Asia WGS AF: 0.512 AC: 1779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs7071471; hg19: chr10-51503335;