6-136995447-G-C

Variant names:

• chr6-136995447-G-C
• rs1547091
• ENST00000458017.1:n.99+179G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000458017.1(ENSG00000235399):​n.99+179G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,172 control chromosomes in the GnomAD database, including 57,755 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 0.84 (57755 hom., cov: 32)
• Consequence: ENSG00000235399 ENST00000458017.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

Genes affected

ENSG00000235399 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 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
ENSG00000235399	ENST00000458017.1	n.99+179G>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127145 AN: 152054 Hom.: 57756 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.977

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.997

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.952

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.836 AC: 127165 AN: 152172 Hom.: 57755 Cov.: 32 AF XY: 0.841 AC XY: 62575 AN XY: 74430

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.977

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.997

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.856

Alfa AF: 0.868 Hom.: 3810

Bravo AF: 0.812

Asia WGS AF: 0.934 AC: 3249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547091; hg19: chr6-137316584;