chr11-103533183-C-T

Variant names:

• chr11-103533183-C-T
• rs7117196
• ENST00000827359.1:n.120-3008G>A

Variant summary

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

The ENST00000827359.1(ENSG00000307600):​n.120-3008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,022 control chromosomes in the GnomAD database, including 19,382 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 0.47 (19382 hom., cov: 32)
• Consequence: ENSG00000307600 ENST00000827359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 6 publications found

Genes affected

ENSG00000307600 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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
ENSG00000307600	ENST00000827359.1	n.120-3008G>A		intron_variant	Intron 1 of 2
ENSG00000307600	ENST00000827360.1	n.92+3226G>A		intron_variant	Intron 1 of 1
ENSG00000307600	ENST00000827363.1	n.92-3008G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71732 AN: 151904 Hom.: 19378 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.472 AC: 71755 AN: 152022 Hom.: 19382 Cov.: 32 AF XY: 0.467 AC XY: 34690 AN XY: 74314

African (AFR) AF: 0.224 AC: 9284 AN: 41468

American (AMR) AF: 0.441 AC: 6742 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2061 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1221 AN: 5158

South Asian (SAS) AF: 0.436 AC: 2102 AN: 4826

European-Finnish (FIN) AF: 0.567 AC: 5978 AN: 10548

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.626 AC: 42534 AN: 67964

Other (OTH) AF: 0.509 AC: 1073 AN: 2106

Alfa AF: 0.587 Hom.: 32680

Bravo AF: 0.452

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.79
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs7117196; hg19: chr11-103403911; COSMIC: COSV53887172;