11-92965261-C-G

Variant names:

• chr11-92965261-C-G
• rs10830962
• ENST00000532770.2:n.266-536C>G

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.266-536C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,026 control chromosomes in the GnomAD database, including 21,683 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 0.51 (21683 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 86 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532770.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254874	ENST00000532770.2	TSL:2	n.266-536C>G		intron	N/A
	ENSG00000254874	ENST00000749785.1		n.248-536C>G		intron	N/A
	ENSG00000254874	ENST00000749786.1		n.307-536C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76775 AN: 151908 Hom.: 21640 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.506 AC: 76870 AN: 152026 Hom.: 21683 Cov.: 32 AF XY: 0.502 AC XY: 37314 AN XY: 74284

African (AFR) AF: 0.775 AC: 32155 AN: 41500

American (AMR) AF: 0.371 AC: 5659 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2278 AN: 5172

South Asian (SAS) AF: 0.515 AC: 2476 AN: 4810

European-Finnish (FIN) AF: 0.393 AC: 4141 AN: 10540

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27088 AN: 67958

Other (OTH) AF: 0.489 AC: 1031 AN: 2110

Alfa AF: 0.392 Hom.: 6228

Bravo AF: 0.515

Asia WGS AF: 0.434 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.48
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs10830962; hg19: chr11-92698427;