chr6-166920485-A-G

Variant names:

• chr6-166920485-A-G
• rs9355606
• ENST00000507747.1:c.432+13606T>C

Variant summary

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

The ENST00000507747.1(ENSG00000249141):​c.432+13606T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 151,452 control chromosomes in the GnomAD database, including 41,375 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 0.70 (41375 hom., cov: 32)
• Consequence: ENSG00000249141 ENST00000507747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 2 publications found

Genes affected

ENSG00000249141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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
ENSG00000249141	ENST00000507747.1	c.432+13606T>C		intron_variant	Intron 7 of 7	5		ENSP00000426906.1
ENSG00000308175	ENST00000832139.1	n.139-984A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105478 AN: 151336 Hom.: 41371 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.697 AC: 105491 AN: 151452 Hom.: 41375 Cov.: 32 AF XY: 0.703 AC XY: 52075 AN XY: 74088

African (AFR) AF: 0.306 AC: 12634 AN: 41334

American (AMR) AF: 0.823 AC: 12512 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2712 AN: 3462

East Asian (EAS) AF: 0.901 AC: 4673 AN: 5184

South Asian (SAS) AF: 0.816 AC: 3922 AN: 4806

European-Finnish (FIN) AF: 0.881 AC: 9320 AN: 10576

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.847 AC: 57262 AN: 67574

Other (OTH) AF: 0.733 AC: 1542 AN: 2104

Alfa AF: 0.791 Hom.: 146808

Bravo AF: 0.676

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.59
PhyloP100		0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9355606; hg19: chr6-167333973;