rs9504093

Variant names:

• chr6-4426537-G-C
• rs9504093
• ENST00000642310.1:n.962+1846C>G

Variant summary

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

The ENST00000642310.1(ENSG00000284823):​n.962+1846C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,908 control chromosomes in the GnomAD database, including 11,564 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 0.38 (11564 hom., cov: 32)
• Consequence: ENSG00000284823 ENST00000642310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 1 publications found

Genes affected

ENSG00000284823 (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 (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642310.1. 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
	ENSG00000284823	ENST00000642310.1		n.962+1846C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58210 AN: 151788 Hom.: 11560 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.383 AC: 58252 AN: 151908 Hom.: 11564 Cov.: 32 AF XY: 0.386 AC XY: 28690 AN XY: 74244

African (AFR) AF: 0.470 AC: 19475 AN: 41398

American (AMR) AF: 0.403 AC: 6154 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1545 AN: 5164

South Asian (SAS) AF: 0.514 AC: 2480 AN: 4824

European-Finnish (FIN) AF: 0.336 AC: 3537 AN: 10530

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22523 AN: 67946

Other (OTH) AF: 0.406 AC: 854 AN: 2106

Alfa AF: 0.364 Hom.: 1254

Bravo AF: 0.390

Asia WGS AF: 0.414 AC: 1441 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	4.1
DANN	Benign	0.57
PhyloP100		0.64

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: rs9504093;

hg19: chr6-4426771;