rs7102746

Variant names:

• chr11-92933397-T-C
• rs7102746
• ENST00000532770.2:n.146+2391T>C

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.146+2391T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,062 control chromosomes in the GnomAD database, including 33,075 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 0.64 (33075 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 5 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 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+2391T>C		intron_variant	Intron 1 of 3	2
ENSG00000254874	ENST00000749785.1	n.128+2391T>C		intron_variant	Intron 1 of 2
ENSG00000254874	ENST00000749786.1	n.115+2391T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96801 AN: 151944 Hom.: 33026 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.637 AC: 96908 AN: 152062 Hom.: 33075 Cov.: 32 AF XY: 0.635 AC XY: 47169 AN XY: 74324

African (AFR) AF: 0.906 AC: 37613 AN: 41510

American (AMR) AF: 0.586 AC: 8950 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1632 AN: 3468

East Asian (EAS) AF: 0.556 AC: 2856 AN: 5140

South Asian (SAS) AF: 0.506 AC: 2436 AN: 4810

European-Finnish (FIN) AF: 0.521 AC: 5513 AN: 10572

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36036 AN: 67966

Other (OTH) AF: 0.597 AC: 1260 AN: 2112

Alfa AF: 0.557 Hom.: 11880

Bravo AF: 0.654

Asia WGS AF: 0.525 AC: 1828 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	0.60
DANN	Benign	0.64
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7102746; hg19: chr11-92666563;