chr6-168725230-A-G

Variant names:

• chr6-168725230-A-G
• rs196472
• ENST00000746859.1:n.369-1161A>G

Variant summary

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

The ENST00000746859.1(ENSG00000289090):​n.369-1161A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,166 control chromosomes in the GnomAD database, including 44,814 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 0.76 (44814 hom., cov: 32)
• Consequence: ENSG00000289090 ENST00000746859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 1 publications found

Genes affected

ENSG00000289090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746859.1. 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
	ENSG00000289090	ENST00000746859.1		n.369-1161A>G		intron	N/A
	ENSG00000289090	ENST00000746860.1		n.235-1161A>G		intron	N/A
	ENSG00000289090	ENST00000746863.1		n.281-65A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116291 AN: 152048 Hom.: 44808 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.765 AC: 116334 AN: 152166 Hom.: 44814 Cov.: 32 AF XY: 0.769 AC XY: 57207 AN XY: 74378

African (AFR) AF: 0.702 AC: 29155 AN: 41520

American (AMR) AF: 0.769 AC: 11758 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2748 AN: 3472

East Asian (EAS) AF: 0.960 AC: 4949 AN: 5154

South Asian (SAS) AF: 0.911 AC: 4389 AN: 4816

European-Finnish (FIN) AF: 0.801 AC: 8487 AN: 10592

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52203 AN: 68000

Other (OTH) AF: 0.804 AC: 1699 AN: 2112

Alfa AF: 0.771 Hom.: 52282

Bravo AF: 0.758

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
PhyloP100		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs196472;

hg19: chr6-169125339;