rs9472138

Variant names:

• chr6-43844025-C-T
• rs9472138
• ENST00000719551.1:n.315+1392C>T

Variant summary

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

The ENST00000719551.1(ENSG00000283573):​n.315+1392C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,154 control chromosomes in the GnomAD database, including 4,787 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 (4787 hom., cov: 32)
• Consequence: ENSG00000283573 ENST00000719551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 113 publications found

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719551.1. 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
	ENSG00000283573	ENST00000719551.1		n.315+1392C>T		intron	N/A
	ENSG00000283573	ENST00000719552.1		n.403+1392C>T		intron	N/A
	ENSG00000283573	ENST00000719558.1		n.199-1251C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37071 AN: 152038 Hom.: 4784 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.244 AC: 37097 AN: 152154 Hom.: 4787 Cov.: 32 AF XY: 0.243 AC XY: 18103 AN XY: 74380

African (AFR) AF: 0.190 AC: 7869 AN: 41516

American (AMR) AF: 0.202 AC: 3092 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3468

East Asian (EAS) AF: 0.131 AC: 679 AN: 5186

South Asian (SAS) AF: 0.192 AC: 927 AN: 4820

European-Finnish (FIN) AF: 0.307 AC: 3244 AN: 10564

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19494 AN: 67984

Other (OTH) AF: 0.267 AC: 564 AN: 2112

Alfa AF: 0.269 Hom.: 26634

Bravo AF: 0.234

Asia WGS AF: 0.182 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.55
PhyloP100		-0.070

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: rs9472138;

hg19: chr6-43811762;