rs1407846

Variant names:

• chr9-108383173-G-C
• rs1407846
• ENST00000826308.1:n.98-7577C>G

Variant summary

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

The ENST00000826308.1(ENSG00000307437):​n.98-7577C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0519 in 152,248 control chromosomes in the GnomAD database, including 336 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 0.052 (336 hom., cov: 32)
• Consequence: ENSG00000307437 ENST00000826308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 1 publications found

Genes affected

ENSG00000307437 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0998 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826308.1. 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
	ENSG00000307437	ENST00000826308.1		n.98-7577C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0518 AC: 7885 AN: 152130 Hom.: 337 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0315

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0519 AC: 7900 AN: 152248 Hom.: 336 Cov.: 32 AF XY: 0.0526 AC XY: 3912 AN XY: 74436

African (AFR) AF: 0.102 AC: 4250 AN: 41526

American (AMR) AF: 0.0404 AC: 618 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0765 AC: 369 AN: 4824

European-Finnish (FIN) AF: 0.0205 AC: 218 AN: 10616

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0315 AC: 2143 AN: 68032

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0411 Hom.: 13

Bravo AF: 0.0538

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		0.013

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: rs1407846;

hg19: chr9-111145453;