rs255592

Variant names:

• chr5-73991586-C-A
• rs255592
• ENST00000803880.1:n.703+8948C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-73991586-C-A
• chr5-73991586-C-G
• chr5-73991586-C-T

Variant summary

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

The ENST00000803880.1(ENSG00000304504):​n.703+8948C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,018 control chromosomes in the GnomAD database, including 40,961 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 0.73 (40961 hom., cov: 32)
• Consequence: ENSG00000304504 ENST00000803880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 3 publications found

Genes affected

ENSG00000304504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803880.1. 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
	ENSG00000304504	ENST00000803880.1		n.703+8948C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111217 AN: 151900 Hom.: 40924 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.732 AC: 111309 AN: 152018 Hom.: 40961 Cov.: 32 AF XY: 0.734 AC XY: 54507 AN XY: 74296

African (AFR) AF: 0.774 AC: 32094 AN: 41476

American (AMR) AF: 0.812 AC: 12391 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2643 AN: 3470

East Asian (EAS) AF: 0.539 AC: 2784 AN: 5168

South Asian (SAS) AF: 0.616 AC: 2960 AN: 4806

European-Finnish (FIN) AF: 0.730 AC: 7711 AN: 10566

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48206 AN: 67954

Other (OTH) AF: 0.750 AC: 1582 AN: 2110

Alfa AF: 0.720 Hom.: 120940

Bravo AF: 0.746

Asia WGS AF: 0.642 AC: 2231 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.52
PhyloP100		-0.96

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: rs255592;

hg19: chr5-73287411;