4-189113137-T-C

Variant names:

• chr4-189113137-T-C
• rs6841266
• ENST00000776569.1:n.552+11102A>G

Variant summary

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

The ENST00000776569.1(ENSG00000301147):​n.552+11102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,116 control chromosomes in the GnomAD database, including 35,022 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 0.67 (35022 hom., cov: 33)
• Consequence: ENSG00000301147 ENST00000776569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 4 publications found

Genes affected

ENSG00000301147 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776569.1. 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
	ENSG00000301147	ENST00000776569.1		n.552+11102A>G		intron	N/A
	ENSG00000301147	ENST00000776579.1		n.265+11102A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102480 AN: 151994 Hom.: 34990 Cov.: 33

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.674 AC: 102556 AN: 152116 Hom.: 35022 Cov.: 33 AF XY: 0.670 AC XY: 49855 AN XY: 74370

African (AFR) AF: 0.724 AC: 30045 AN: 41512

American (AMR) AF: 0.551 AC: 8416 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2362 AN: 3472

East Asian (EAS) AF: 0.454 AC: 2342 AN: 5160

South Asian (SAS) AF: 0.599 AC: 2889 AN: 4820

European-Finnish (FIN) AF: 0.668 AC: 7062 AN: 10570

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47221 AN: 67984

Other (OTH) AF: 0.685 AC: 1449 AN: 2116

Alfa AF: 0.686 Hom.: 151086

Bravo AF: 0.662

Asia WGS AF: 0.577 AC: 2004 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.9
DANN	Benign	0.84
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs6841266; hg19: chr4-190034291;