rs9357347

Variant names:

• chr6-41182853-A-C
• rs9357347
• ENST00000736323.1:n.410+258T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-41182853-A-C
• chr6-41182853-A-T

Variant summary

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

The ENST00000736323.1(ENSG00000296086):​n.410+258T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,048 control chromosomes in the GnomAD database, including 5,299 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 (5299 hom., cov: 32)
• Consequence: ENSG00000296086 ENST00000736323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 14 publications found

Genes affected

ENSG00000296086 (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 (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736323.1. 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
	ENSG00000296086	ENST00000736323.1		n.410+258T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36747 AN: 151930 Hom.: 5296 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.242 AC: 36756 AN: 152048 Hom.: 5299 Cov.: 32 AF XY: 0.245 AC XY: 18233 AN XY: 74310

African (AFR) AF: 0.0750 AC: 3112 AN: 41492

American (AMR) AF: 0.319 AC: 4870 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1287 AN: 5174

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4822

European-Finnish (FIN) AF: 0.311 AC: 3286 AN: 10560

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20703 AN: 67956

Other (OTH) AF: 0.245 AC: 517 AN: 2106

Alfa AF: 0.283 Hom.: 5183

Bravo AF: 0.233

Asia WGS AF: 0.307 AC: 1067 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	0.12
DANN	Benign	0.73
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9357347; hg19: chr6-41150591;