rs6859018

Variant names:

• chr5-159309984-G-A
• rs6859018
• ENST00000765301.1:n.221+473C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-159309984-G-A
• chr5-159309984-G-C
• chr5-159309984-G-T

Variant summary

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

The ENST00000765301.1(ENSG00000299638):​n.221+473C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,042 control chromosomes in the GnomAD database, including 6,254 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 0.27 (6254 hom., cov: 32)
• Consequence: ENSG00000299638 ENST00000765301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 16 publications found

Genes affected

ENSG00000299638 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299638	ENST00000765301.1	n.221+473C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41369 AN: 151924 Hom.: 6244 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.272 AC: 41407 AN: 152042 Hom.: 6254 Cov.: 32 AF XY: 0.276 AC XY: 20499 AN XY: 74308

African (AFR) AF: 0.368 AC: 15249 AN: 41456

American (AMR) AF: 0.338 AC: 5164 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2295 AN: 5166

South Asian (SAS) AF: 0.362 AC: 1737 AN: 4798

European-Finnish (FIN) AF: 0.178 AC: 1888 AN: 10584

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.200 AC: 13625 AN: 67980

Other (OTH) AF: 0.290 AC: 612 AN: 2112

Alfa AF: 0.279 Hom.: 1728

Bravo AF: 0.291

Asia WGS AF: 0.428 AC: 1485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.73
PhyloP100		0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6859018; hg19: chr5-158736992;