rs9468925

Variant names:

• chr6-31291060-G-A
• rs9468925
• ENST00000755297.1:n.32+19954G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31291060-G-A
• chr6-31291060-G-C
• chr6-31291060-G-T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+19954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,078 control chromosomes in the GnomAD database, including 15,400 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 0.44 (15400 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 60 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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+19954G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67272 AN: 151958 Hom.: 15374 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.443 AC: 67337 AN: 152078 Hom.: 15400 Cov.: 32 AF XY: 0.449 AC XY: 33335 AN XY: 74310

African (AFR) AF: 0.551 AC: 22869 AN: 41474

American (AMR) AF: 0.479 AC: 7329 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3468

East Asian (EAS) AF: 0.377 AC: 1954 AN: 5178

South Asian (SAS) AF: 0.459 AC: 2215 AN: 4824

European-Finnish (FIN) AF: 0.494 AC: 5208 AN: 10546

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25184 AN: 67976

Other (OTH) AF: 0.443 AC: 936 AN: 2114

Alfa AF: 0.396 Hom.: 43087

Bravo AF: 0.446

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.72
PhyloP100		-0.42

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: rs9468925;

hg19: chr6-31258837;