rs6416582

Variant names:

• chr15-93193716-A-C
• rs6416582
• ENST00000711606.1:n.616-18564A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-93193716-A-C
• chr15-93193716-A-G
• chr15-93193716-A-T

Variant summary

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

The ENST00000711606.1(ENSG00000257060):​n.616-18564A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,032 control chromosomes in the GnomAD database, including 8,147 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 0.31 (8147 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000711606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 4 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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
ENSG00000257060	ENST00000711606.1	n.616-18564A>C		intron_variant	Intron 6 of 11
ENSG00000257060	ENST00000791023.1	n.312+23165A>C		intron_variant	Intron 3 of 6
ENSG00000257060	ENST00000791051.1	n.525+23165A>C		intron_variant	Intron 5 of 7
ENSG00000257060	ENST00000791055.1	n.462+23165A>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47788 AN: 151914 Hom.: 8122 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.315 AC: 47851 AN: 152032 Hom.: 8147 Cov.: 32 AF XY: 0.309 AC XY: 22989 AN XY: 74324

African (AFR) AF: 0.436 AC: 18083 AN: 41430

American (AMR) AF: 0.273 AC: 4169 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1022 AN: 5182

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4816

European-Finnish (FIN) AF: 0.190 AC: 2012 AN: 10564

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19006 AN: 67976

Other (OTH) AF: 0.327 AC: 689 AN: 2108

Alfa AF: 0.294 Hom.: 29544

Bravo AF: 0.324

Asia WGS AF: 0.252 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6416582; hg19: chr15-93736945;