rs13106777

Variant names:

• chr4-189164577-A-G
• rs13106777
• ENST00000776569.1:n.299+6149T>C

Variant summary

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

The ENST00000776569.1(ENSG00000301147):​n.299+6149T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,246 control chromosomes in the GnomAD database, including 729 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 0.086 (729 hom., cov: 33)
• Consequence: ENSG00000301147 ENST00000776569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 2 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=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 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
ENSG00000301147	ENST00000776569.1	n.299+6149T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13172 AN: 152128 Hom.: 727 Cov.: 33

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0865 AC: 13163 AN: 152246 Hom.: 729 Cov.: 33 AF XY: 0.0862 AC XY: 6417 AN XY: 74444

African (AFR) AF: 0.0237 AC: 984 AN: 41584

American (AMR) AF: 0.0804 AC: 1229 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0778 AC: 376 AN: 4830

European-Finnish (FIN) AF: 0.119 AC: 1264 AN: 10604

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8609 AN: 67966

Other (OTH) AF: 0.102 AC: 215 AN: 2116

Alfa AF: 0.121 Hom.: 1814

Bravo AF: 0.0813

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.47
DANN	Benign	0.59
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs13106777; hg19: chr4-190085731;