1-86523026-G-A

Variant names:

• chr1-86523026-G-A
• rs2791473
• ENST00000760441.1:n.482C>T

Variant summary

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

The ENST00000760441.1(ENSG00000299097):​n.482C>T 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 0.471 in 152,068 control chromosomes in the GnomAD database, including 18,944 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 (18944 hom., cov: 32)
• Consequence: ENSG00000299097 ENST00000760441.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665
• Publications: 6 publications found

Genes affected

ENSG00000299097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000760441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299097	ENST00000760441.1		n.482C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000299097	ENST00000760439.1		n.259+215C>T		intron	N/A
	ENSG00000299097	ENST00000760440.1		n.292+187C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71547 AN: 151950 Hom.: 18929 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.471 AC: 71587 AN: 152068 Hom.: 18944 Cov.: 32 AF XY: 0.476 AC XY: 35358 AN XY: 74344

African (AFR) AF: 0.212 AC: 8772 AN: 41470

American (AMR) AF: 0.585 AC: 8938 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1778 AN: 3466

East Asian (EAS) AF: 0.376 AC: 1940 AN: 5162

South Asian (SAS) AF: 0.471 AC: 2272 AN: 4822

European-Finnish (FIN) AF: 0.654 AC: 6918 AN: 10570

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39226 AN: 67974

Other (OTH) AF: 0.481 AC: 1016 AN: 2114

Alfa AF: 0.530 Hom.: 70472

Bravo AF: 0.454

Asia WGS AF: 0.381 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		0.67

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2791473;

hg19: chr1-86988709;