rs12576973

Variant names:

• chr11-127388747-G-T
• rs12576973
• ENST00000822754.1:n.105+25488G>T

Variant summary

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

The ENST00000822754.1(ENSG00000307024):​n.105+25488G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,146 control chromosomes in the GnomAD database, including 2,051 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 0.15 (2051 hom., cov: 33)
• Consequence: ENSG00000307024 ENST00000822754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 1 publications found

Genes affected

ENSG00000307024 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 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
ENSG00000307024	ENST00000822754.1	n.105+25488G>T		intron_variant	Intron 1 of 3
ENSG00000307024	ENST00000822755.1	n.142+25444G>T		intron_variant	Intron 1 of 2
ENSG00000307024	ENST00000822756.1	n.96+25488G>T		intron_variant	Intron 1 of 2
ENSG00000307024	ENST00000822757.1	n.140+25444G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22646 AN: 152028 Hom.: 2045 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.149 AC: 22661 AN: 152146 Hom.: 2051 Cov.: 33 AF XY: 0.150 AC XY: 11124 AN XY: 74382

African (AFR) AF: 0.241 AC: 9987 AN: 41500

American (AMR) AF: 0.0972 AC: 1486 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3470

East Asian (EAS) AF: 0.170 AC: 879 AN: 5160

South Asian (SAS) AF: 0.256 AC: 1234 AN: 4822

European-Finnish (FIN) AF: 0.103 AC: 1086 AN: 10594

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7013 AN: 68006

Other (OTH) AF: 0.161 AC: 338 AN: 2104

Alfa AF: 0.122 Hom.: 229

Bravo AF: 0.151

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.6
DANN	Benign	0.44
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs12576973; hg19: chr11-127258642;