ENST00000691159.1:n.357+8406C>G

Variant names:

• chr6-170177401-G-C
• rs7453655
• ENST00000691159.1:n.357+8406C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000691159.1(ENSG00000230960):​n.357+8406C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.018 (180 hom., cov: 20)
• Consequence: ENSG00000230960 ENST00000691159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983
• Publications: 2 publications found

Genes affected

ENSG00000230960 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0177 (1536/86712) while in subpopulation NFE AF = 0.0257 (1036/40324). AF 95% confidence interval is 0.0244. There are 180 homozygotes in GnomAd4. There are 693 alleles in the male GnomAd4 subpopulation. Median coverage is 20. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 180 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691159.1. 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
	ENSG00000230960	ENST00000691159.1		n.357+8406C>G		intron	N/A
	ENSG00000230960	ENST00000701993.1		n.382+8337C>G		intron	N/A
	ENSG00000230960	ENST00000843770.1		n.475+8406C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0177 AC: 1537 AN: 86652 Hom.: 180 Cov.: 20

Gnomad AFR AF: 0.00993

Gnomad AMI AF: 0.0226

Gnomad AMR AF: 0.0152

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.00793

Gnomad MID AF: 0.0352

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0168

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

GnomAD4 genome AF: 0.0177 AC: 1536 AN: 86712 Hom.: 180 Cov.: 20 AF XY: 0.0166 AC XY: 693 AN XY: 41854

African (AFR) AF: 0.00991 AC: 229 AN: 23112

American (AMR) AF: 0.0152 AC: 120 AN: 7908

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 44 AN: 2124

East Asian (EAS) AF: 0.00 AC: 0 AN: 3230

South Asian (SAS) AF: 0.0104 AC: 27 AN: 2584

European-Finnish (FIN) AF: 0.00793 AC: 45 AN: 5676

Middle Eastern (MID) AF: 0.0391 AC: 5 AN: 128

European-Non Finnish (NFE) AF: 0.0257 AC: 1036 AN: 40324

Other (OTH) AF: 0.0167 AC: 19 AN: 1140

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.35
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs7453655; hg19: chr6-170492625;