6-136995447-G-C

Variant names:

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

Variant summary

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

The ENST00000826689.1(ENSG00000235399):​n.225+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 ENST00000826689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279
• Publications: 0 publications found

Genes affected

ENSG00000235399 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826689.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235399	ENST00000458017.1	TSL:5	n.99+179G>C		intron	N/A
	ENSG00000235399	ENST00000826689.1		n.225+179G>C		intron	N/A

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

African (AFR) AF: 0.439 AC: 18194 AN: 41414

American (AMR) AF: 0.930 AC: 14233 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.977 AC: 3392 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5186 AN: 5190

South Asian (SAS) AF: 0.997 AC: 4815 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10615 AN: 10616

Middle Eastern (MID) AF: 0.959 AC: 280 AN: 292

European-Non Finnish (NFE) AF: 0.996 AC: 67734 AN: 68032

Other (OTH) AF: 0.856 AC: 1804 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.63
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1547091; hg19: chr6-137316584;