rs6580586

Variant names:

• chr5-148863160-A-C
• rs6580586
• ENST00000798472.1:n.377-9344A>C

Variant summary

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

The ENST00000798472.1(ENSG00000303969):​n.377-9344A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,092 control chromosomes in the GnomAD database, including 7,675 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 0.24 (7675 hom., cov: 32)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 10 publications found

Genes affected

ENSG00000303969 (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 (AFR) allele frequency at 95% confidence interval = 0.573 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
ENSG00000303969	ENST00000798472.1	n.377-9344A>C		intron_variant	Intron 3 of 4
ENSG00000303969	ENST00000798473.1	n.350-9344A>C		intron_variant	Intron 3 of 4
ENSG00000303982	ENST00000798634.1	n.153-537A>C		intron_variant	Intron 1 of 1
ENSG00000303982	ENST00000798635.1	n.136-537A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36344 AN: 151974 Hom.: 7664 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.239 AC: 36386 AN: 152092 Hom.: 7675 Cov.: 32 AF XY: 0.235 AC XY: 17466 AN XY: 74354

African (AFR) AF: 0.579 AC: 23996 AN: 41434

American (AMR) AF: 0.124 AC: 1891 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3464

East Asian (EAS) AF: 0.171 AC: 884 AN: 5168

South Asian (SAS) AF: 0.126 AC: 606 AN: 4826

European-Finnish (FIN) AF: 0.108 AC: 1145 AN: 10600

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6888 AN: 68000

Other (OTH) AF: 0.209 AC: 441 AN: 2112

Alfa AF: 0.138 Hom.: 4308

Bravo AF: 0.257

Asia WGS AF: 0.168 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6580586; hg19: chr5-148242723;