11-92938855-G-T

Variant names:

• chr11-92938855-G-T
• rs7112766
• ENST00000532770.2:n.146+7849G>T

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.146+7849G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,730 control chromosomes in the GnomAD database, including 14,936 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 0.42 (14936 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 9 publications found

Genes affected

ENSG00000254874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 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
ENSG00000254874	ENST00000532770.2	n.146+7849G>T		intron_variant	Intron 1 of 3	2
ENSG00000254874	ENST00000749785.1	n.128+7849G>T		intron_variant	Intron 1 of 2
ENSG00000254874	ENST00000749786.1	n.115+7849G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.422 AC: 63941 AN: 151610 Hom.: 14902 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.422 AC: 64030 AN: 151730 Hom.: 14936 Cov.: 32 AF XY: 0.422 AC XY: 31301 AN XY: 74182

African (AFR) AF: 0.633 AC: 26191 AN: 41398

American (AMR) AF: 0.297 AC: 4526 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1067 AN: 3422

East Asian (EAS) AF: 0.446 AC: 2302 AN: 5166

South Asian (SAS) AF: 0.459 AC: 2205 AN: 4802

European-Finnish (FIN) AF: 0.375 AC: 3961 AN: 10570

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22322 AN: 67788

Other (OTH) AF: 0.395 AC: 835 AN: 2116

Alfa AF: 0.263 Hom.: 884

Bravo AF: 0.423

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.44
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7112766; hg19: chr11-92672021;