rs9308447

Variant names:

• chr1-9372331-C-T
• rs9308447
• ENST00000735987.1:n.345G>A

Variant summary

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

The ENST00000735987.1(ENSG00000296056):​n.345G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,022 control chromosomes in the GnomAD database, including 6,224 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 0.27 (6224 hom., cov: 31)
• Consequence: ENSG00000296056 ENST00000735987.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 9 publications found

Genes affected

ENSG00000296056 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000735987.1. 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
	ENSG00000296056	ENST00000735987.1		n.345G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000296056	ENST00000735988.1		n.203G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000296073	ENST00000736034.1		n.533-758C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40805 AN: 151904 Hom.: 6210 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.269 AC: 40869 AN: 152022 Hom.: 6224 Cov.: 31 AF XY: 0.265 AC XY: 19720 AN XY: 74324

African (AFR) AF: 0.411 AC: 17004 AN: 41422

American (AMR) AF: 0.296 AC: 4519 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1041 AN: 5164

South Asian (SAS) AF: 0.135 AC: 648 AN: 4814

European-Finnish (FIN) AF: 0.129 AC: 1366 AN: 10598

Middle Eastern (MID) AF: 0.228 AC: 66 AN: 290

European-Non Finnish (NFE) AF: 0.217 AC: 14721 AN: 67982

Other (OTH) AF: 0.253 AC: 533 AN: 2106

Alfa AF: 0.245 Hom.: 9614

Bravo AF: 0.285

Asia WGS AF: 0.177 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.43
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: rs9308447;

hg19: chr1-9432390;