11-127392093-C-T

Variant names:

• chr11-127392093-C-T
• rs12577873
• ENST00000822754.1:n.105+28834C>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+28834C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,170 control chromosomes in the GnomAD database, including 1,988 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 (1988 hom., cov: 32)
• Consequence: ENSG00000307024 ENST00000822754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 2 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=-1.11).
• 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+28834C>T		intron_variant	Intron 1 of 3
ENSG00000307024	ENST00000822755.1	n.142+28790C>T		intron_variant	Intron 1 of 2
ENSG00000307024	ENST00000822756.1	n.96+28834C>T		intron_variant	Intron 1 of 2
ENSG00000307024	ENST00000822757.1	n.140+28790C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22391 AN: 152052 Hom.: 1983 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.102

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: 0.147 AC: 22399 AN: 152170 Hom.: 1988 Cov.: 32 AF XY: 0.148 AC XY: 10992 AN XY: 74388

African (AFR) AF: 0.234 AC: 9729 AN: 41508

American (AMR) AF: 0.0966 AC: 1478 AN: 15300

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

East Asian (EAS) AF: 0.170 AC: 877 AN: 5150

South Asian (SAS) AF: 0.256 AC: 1233 AN: 4824

European-Finnish (FIN) AF: 0.102 AC: 1083 AN: 10594

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

European-Non Finnish (NFE) AF: 0.103 AC: 7022 AN: 68004

Other (OTH) AF: 0.160 AC: 339 AN: 2114

Alfa AF: 0.118 Hom.: 203

Bravo AF: 0.149

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.036
DANN	Benign	0.68
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs12577873; hg19: chr11-127261988;