chr9-31619336-G-A

Variant names:

• chr9-31619336-G-A
• rs1412340
• ENST00000804476.1:n.183+14838C>T

Variant summary

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

The ENST00000804476.1(ENSG00000304547):​n.183+14838C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,838 control chromosomes in the GnomAD database, including 6,789 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 0.29 (6789 hom., cov: 32)
• Consequence: ENSG00000304547 ENST00000804476.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.865
• Publications: 3 publications found

Genes affected

ENSG00000304547 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804476.1. 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
	ENSG00000304547	ENST00000804476.1		n.183+14838C>T		intron	N/A
	ENSG00000304547	ENST00000804478.1		n.75+14838C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44477 AN: 151720 Hom.: 6778 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.293 AC: 44510 AN: 151838 Hom.: 6789 Cov.: 32 AF XY: 0.293 AC XY: 21738 AN XY: 74196

African (AFR) AF: 0.355 AC: 14712 AN: 41442

American (AMR) AF: 0.350 AC: 5325 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3464

East Asian (EAS) AF: 0.118 AC: 607 AN: 5140

South Asian (SAS) AF: 0.185 AC: 892 AN: 4816

European-Finnish (FIN) AF: 0.281 AC: 2968 AN: 10564

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18234 AN: 67890

Other (OTH) AF: 0.308 AC: 649 AN: 2110

Alfa AF: 0.244 Hom.: 1179

Bravo AF: 0.305

Asia WGS AF: 0.176 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.37
PhyloP100		-0.86

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: rs1412340;

hg19: chr9-31619334;