11-124085759-A-G

Variant names:

• chr11-124085759-A-G
• rs1893767
• ENST00000837378.1:n.290+623T>C

Variant summary

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

The ENST00000837378.1(ENSG00000308936):​n.290+623T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,206 control chromosomes in the GnomAD database, including 2,139 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 0.13 (2139 hom., cov: 33)
• Consequence: ENSG00000308936 ENST00000837378.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 5 publications found

Genes affected

ENSG00000308936 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837378.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308936	ENST00000837378.1		n.290+623T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19573 AN: 152088 Hom.: 2142 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.0826

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0434

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.129 AC: 19590 AN: 152206 Hom.: 2139 Cov.: 33 AF XY: 0.130 AC XY: 9650 AN XY: 74428

African (AFR) AF: 0.289 AC: 12005 AN: 41486

American (AMR) AF: 0.111 AC: 1694 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1399 AN: 5184

South Asian (SAS) AF: 0.0824 AC: 398 AN: 4828

European-Finnish (FIN) AF: 0.0497 AC: 527 AN: 10614

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0433 AC: 2948 AN: 68010

Other (OTH) AF: 0.108 AC: 227 AN: 2110

Alfa AF: 0.0736 Hom.: 3171

Bravo AF: 0.142

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs1893767; hg19: chr11-123956466;