rs9307481

Variant names:

• chr4-119854993-C-T
• rs9307481
• ENST00000770494.1:n.348C>T

Variant summary

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

The ENST00000770494.1(ENSG00000300267):​n.348C>T 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 0.0918 in 152,042 control chromosomes in the GnomAD database, including 1,587 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 0.092 (1587 hom., cov: 32)
• Consequence: ENSG00000300267 ENST00000770494.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 0 publications found

Genes affected

ENSG00000300267 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770494.1. 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
	ENSG00000300267	ENST00000770494.1		n.348C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000300267	ENST00000770495.1		n.351C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000300267	ENST00000770496.1		n.191C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13927 AN: 151924 Hom.: 1581 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0565

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00686

Gnomad FIN AF: 0.00340

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.0918 AC: 13965 AN: 152042 Hom.: 1587 Cov.: 32 AF XY: 0.0886 AC XY: 6580 AN XY: 74308

African (AFR) AF: 0.276 AC: 11442 AN: 41420

American (AMR) AF: 0.0564 AC: 861 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3472

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5166

South Asian (SAS) AF: 0.00666 AC: 32 AN: 4806

European-Finnish (FIN) AF: 0.00340 AC: 36 AN: 10590

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0185 AC: 1257 AN: 68000

Other (OTH) AF: 0.0882 AC: 186 AN: 2108

Alfa AF: 0.0493 Hom.: 239

Bravo AF: 0.106

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.052
DANN	Benign	0.65
PhyloP100		-1.9

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: rs9307481;

hg19: chr4-120776148;