11-4409864-C-G

Variant names:

• chr11-4409864-C-G
• rs1376681
• ENST00000641797.5:n.386+15699C>G

Variant summary

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

The ENST00000641797.5(ENSG00000291144):​n.386+15699C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,960 control chromosomes in the GnomAD database, including 19,725 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 0.50 (19725 hom., cov: 32)
• Consequence: ENSG00000291144 ENST00000641797.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 0 publications found

Genes affected

ENSG00000291144 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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
ENSG00000291144	ENST00000641797.5	n.386+15699C>G		intron_variant	Intron 1 of 2
ENSG00000291144	ENST00000685350.2	n.391+15699C>G		intron_variant	Intron 1 of 2
ENSG00000291144	ENST00000687315.2	n.430-535C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76638 AN: 151840 Hom.: 19694 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.505 AC: 76734 AN: 151960 Hom.: 19725 Cov.: 32 AF XY: 0.506 AC XY: 37559 AN XY: 74286

African (AFR) AF: 0.542 AC: 22440 AN: 41428

American (AMR) AF: 0.542 AC: 8287 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3492 AN: 5154

South Asian (SAS) AF: 0.436 AC: 2098 AN: 4814

European-Finnish (FIN) AF: 0.490 AC: 5168 AN: 10548

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32613 AN: 67958

Other (OTH) AF: 0.467 AC: 984 AN: 2108

Alfa AF: 0.371 Hom.: 996

Bravo AF: 0.512

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.68
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1376681; hg19: chr11-4431094;