rs9379174

Variant names:

• chr6-8222541-C-T
• rs9379174
• ENST00000439891.3:n.61-7573C>T

Variant summary

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

The ENST00000439891.3(ENSG00000232234):​n.61-7573C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,052 control chromosomes in the GnomAD database, including 4,452 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 0.24 (4452 hom., cov: 32)
• Consequence: ENSG00000232234 ENST00000439891.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 5 publications found

Genes affected

ENSG00000232234 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439891.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232234	ENST00000439891.3	TSL:5	n.61-7573C>T		intron	N/A
	ENSG00000232234	ENST00000642149.1		n.207-16390C>T		intron	N/A
	ENSG00000232234	ENST00000643749.1		n.143-16390C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36312 AN: 151934 Hom.: 4451 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.239 AC: 36330 AN: 152052 Hom.: 4452 Cov.: 32 AF XY: 0.236 AC XY: 17562 AN XY: 74332

African (AFR) AF: 0.259 AC: 10728 AN: 41450

American (AMR) AF: 0.226 AC: 3454 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3472

East Asian (EAS) AF: 0.366 AC: 1885 AN: 5156

South Asian (SAS) AF: 0.194 AC: 935 AN: 4824

European-Finnish (FIN) AF: 0.193 AC: 2044 AN: 10572

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15676 AN: 67986

Other (OTH) AF: 0.263 AC: 554 AN: 2108

Alfa AF: 0.232 Hom.: 17498

Bravo AF: 0.241

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.63
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs9379174; hg19: chr6-8222774;