rs2540477

Variant names:

• chr12-96043776-G-A
• rs2540477
• ENST00000824362.1:n.272-3842G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-96043776-G-A
• chr12-96043776-G-C
• chr12-96043776-G-T

Variant summary

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

The ENST00000824362.1(ENSG00000307169):​n.272-3842G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,008 control chromosomes in the GnomAD database, including 44,596 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 0.76 (44596 hom., cov: 30)
• Consequence: ENSG00000307169 ENST00000824362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 13 publications found

Genes affected

ENSG00000307169 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 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
ENSG00000307169	ENST00000824362.1	n.272-3842G>A		intron_variant	Intron 1 of 2
ENSG00000307169	ENST00000824363.1	n.97+8277G>A		intron_variant	Intron 1 of 1
ENSG00000307169	ENST00000824364.1	n.143-3842G>A		intron_variant	Intron 1 of 2
ENSG00000307169	ENST00000824365.1	n.225-254G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115564 AN: 151890 Hom.: 44561 Cov.: 30

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.761 AC: 115645 AN: 152008 Hom.: 44596 Cov.: 30 AF XY: 0.758 AC XY: 56292 AN XY: 74308

African (AFR) AF: 0.829 AC: 34346 AN: 41440

American (AMR) AF: 0.592 AC: 9034 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2572 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2299 AN: 5160

South Asian (SAS) AF: 0.808 AC: 3900 AN: 4824

European-Finnish (FIN) AF: 0.817 AC: 8629 AN: 10568

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.771 AC: 52438 AN: 67974

Other (OTH) AF: 0.722 AC: 1522 AN: 2108

Alfa AF: 0.758 Hom.: 132441

Bravo AF: 0.741

Asia WGS AF: 0.648 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.45
PhyloP100		-0.73
PromoterAI		-0.024	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2540477; hg19: chr12-96437554;