rs2791473

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-86523026-G-A
• chr1-86523026-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904210	XR_007066206.1	n.225+4346C>T		intron_variant	Intron 1 of 2
LOC105378826	XR_947556.2	n.572-189G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299097	ENST00000760441.1	n.482C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000299097	ENST00000760439.1	n.259+215C>T		intron_variant	Intron 1 of 1
ENSG00000299097	ENST00000760440.1	n.292+187C>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs2791473; hg19: chr1-86988709;