1-175151579-G-A

Variant names:

• chr1-175151579-G-A
• rs10912899
• ENST00000785604.1:n.381+396G>A

Variant summary

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

The ENST00000785604.1(ENSG00000302295):​n.381+396G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,912 control chromosomes in the GnomAD database, including 17,236 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 (17236 hom., cov: 30)
• Consequence: ENSG00000302295 ENST00000785604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 7 publications found

Genes affected

ENSG00000302295 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785604.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302295	ENST00000785604.1		n.381+396G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71197 AN: 151794 Hom.: 17204 Cov.: 30

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.469 AC: 71289 AN: 151912 Hom.: 17236 Cov.: 30 AF XY: 0.473 AC XY: 35117 AN XY: 74238

African (AFR) AF: 0.559 AC: 23172 AN: 41420

American (AMR) AF: 0.569 AC: 8685 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1889 AN: 3468

East Asian (EAS) AF: 0.553 AC: 2858 AN: 5166

South Asian (SAS) AF: 0.502 AC: 2417 AN: 4812

European-Finnish (FIN) AF: 0.405 AC: 4274 AN: 10542

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26360 AN: 67918

Other (OTH) AF: 0.477 AC: 1006 AN: 2108

Alfa AF: 0.432 Hom.: 25519

Bravo AF: 0.488

Asia WGS AF: 0.529 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.90
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs10912899; hg19: chr1-175120715;