rs9468937

Variant names:

• chr6-31302341-C-A
• rs9468937
• ENST00000755297.1:n.32+31235C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31302341-C-A
• chr6-31302341-C-G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+31235C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,002 control chromosomes in the GnomAD database, including 20,576 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 0.51 (20576 hom., cov: 29)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 11 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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
	ENSG00000298396	ENST00000755297.1		n.32+31235C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77264 AN: 150884 Hom.: 20559 Cov.: 29

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.512 AC: 77323 AN: 151002 Hom.: 20576 Cov.: 29 AF XY: 0.516 AC XY: 38100 AN XY: 73774

African (AFR) AF: 0.623 AC: 25600 AN: 41098

American (AMR) AF: 0.477 AC: 7230 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2297 AN: 3460

East Asian (EAS) AF: 0.439 AC: 2247 AN: 5118

South Asian (SAS) AF: 0.604 AC: 2889 AN: 4782

European-Finnish (FIN) AF: 0.498 AC: 5195 AN: 10436

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30078 AN: 67652

Other (OTH) AF: 0.535 AC: 1121 AN: 2094

Alfa AF: 0.368 Hom.: 1304

Bravo AF: 0.513

Asia WGS AF: 0.511 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.20
PhyloP100		-2.9

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: rs9468937;

hg19: chr6-31270118;