rs1265750

Variant names:

• chr2-80724698-T-C
• rs1265750
• ENST00000450290.1:n.469-21004A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-80724698-T-C
• chr2-80724698-T-G

Variant summary

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

The ENST00000450290.1(ENSG00000230975):​n.469-21004A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,136 control chromosomes in the GnomAD database, including 41,349 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 0.71 (41349 hom., cov: 32)
• Consequence: ENSG00000230975 ENST00000450290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 2 publications found

Genes affected

ENSG00000230975 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.839 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
ENSG00000230975	ENST00000450290.1	n.469-21004A>G		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108291 AN: 152018 Hom.: 41345 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.712 AC: 108333 AN: 152136 Hom.: 41349 Cov.: 32 AF XY: 0.713 AC XY: 53024 AN XY: 74382

African (AFR) AF: 0.418 AC: 17339 AN: 41492

American (AMR) AF: 0.789 AC: 12062 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2791 AN: 3468

East Asian (EAS) AF: 0.766 AC: 3938 AN: 5144

South Asian (SAS) AF: 0.588 AC: 2836 AN: 4826

European-Finnish (FIN) AF: 0.882 AC: 9340 AN: 10594

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57467 AN: 68014

Other (OTH) AF: 0.734 AC: 1550 AN: 2112

Alfa AF: 0.800 Hom.: 76707

Bravo AF: 0.695

Asia WGS AF: 0.639 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.9
DANN	Benign	0.83
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1265750; hg19: chr2-80951823;