rs10479469

Variant names:

• chr5-180385668-A-G
• rs10479469
• ENST00000843753.1:n.145-5195T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-180385668-A-G
• chr5-180385668-A-T

Variant summary

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

The ENST00000843753.1(ENSG00000309762):​n.145-5195T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,476 control chromosomes in the GnomAD database, including 10,469 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 0.37 (10469 hom., cov: 28)
• Consequence: ENSG00000309762 ENST00000843753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 13 publications found

Genes affected

ENSG00000309762 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843753.1. 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
	ENSG00000309762	ENST00000843753.1		n.145-5195T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56101 AN: 151360 Hom.: 10458 Cov.: 28

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.371 AC: 56156 AN: 151476 Hom.: 10469 Cov.: 28 AF XY: 0.373 AC XY: 27609 AN XY: 73976

African (AFR) AF: 0.438 AC: 18065 AN: 41266

American (AMR) AF: 0.405 AC: 6170 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3464

East Asian (EAS) AF: 0.351 AC: 1796 AN: 5114

South Asian (SAS) AF: 0.388 AC: 1859 AN: 4786

European-Finnish (FIN) AF: 0.346 AC: 3611 AN: 10424

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22372 AN: 67886

Other (OTH) AF: 0.379 AC: 799 AN: 2110

Alfa AF: 0.343 Hom.: 17304

Bravo AF: 0.383

Asia WGS AF: 0.393 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.63
PhyloP100		-0.14

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: rs10479469;

hg19: chr5-179812668;

COSMIC: COSV56994082;