rs6453460

Variant names:

• chr5-79571726-T-A
• rs6453460
• ENST00000799951.1:n.87-2410T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-79571726-T-A
• chr5-79571726-T-C
• chr5-79571726-T-G

Variant summary

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

The ENST00000799951.1(ENSG00000304127):​n.87-2410T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,102 control chromosomes in the GnomAD database, including 8,251 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 0.28 (8251 hom., cov: 32)
• Consequence: ENSG00000304127 ENST00000799951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 2 publications found

Genes affected

ENSG00000304127 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000799951.1. 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
	ENSG00000304127	ENST00000799951.1		n.87-2410T>A		intron	N/A
	ENSG00000304127	ENST00000799952.1		n.448-2410T>A		intron	N/A
	ENSG00000304127	ENST00000799954.1		n.428-7289T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42972 AN: 151984 Hom.: 8227 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.283 AC: 43057 AN: 152102 Hom.: 8251 Cov.: 32 AF XY: 0.282 AC XY: 20928 AN XY: 74342

African (AFR) AF: 0.523 AC: 21682 AN: 41456

American (AMR) AF: 0.329 AC: 5034 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3464

East Asian (EAS) AF: 0.429 AC: 2223 AN: 5182

South Asian (SAS) AF: 0.191 AC: 920 AN: 4822

European-Finnish (FIN) AF: 0.124 AC: 1318 AN: 10606

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10595 AN: 67980

Other (OTH) AF: 0.278 AC: 588 AN: 2114

Alfa AF: 0.201 Hom.: 549

Bravo AF: 0.315

Asia WGS AF: 0.331 AC: 1147 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.060
PhyloP100		-1.9

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: rs6453460;

hg19: chr5-78867549;