ENST00000846515.1:n.199-2645C>G

Variant names:

• chr5-76846-C-G
• rs6859237
• ENST00000846515.1:n.199-2645C>G

Variant summary

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

The ENST00000846515.1(ENSG00000310001):​n.199-2645C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,030 control chromosomes in the GnomAD database, including 11,506 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 (11506 hom., cov: 33)
• Consequence: ENSG00000310001 ENST00000846515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 0 publications found

Genes affected

ENSG00000310001 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 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
ENSG00000310001	ENST00000846515.1	n.199-2645C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56648 AN: 151912 Hom.: 11466 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.373 AC: 56731 AN: 152030 Hom.: 11506 Cov.: 33 AF XY: 0.370 AC XY: 27509 AN XY: 74316

African (AFR) AF: 0.524 AC: 21708 AN: 41462

American (AMR) AF: 0.358 AC: 5480 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3468

East Asian (EAS) AF: 0.0949 AC: 491 AN: 5174

South Asian (SAS) AF: 0.139 AC: 671 AN: 4828

European-Finnish (FIN) AF: 0.353 AC: 3737 AN: 10586

Middle Eastern (MID) AF: 0.197 AC: 57 AN: 290

European-Non Finnish (NFE) AF: 0.331 AC: 22484 AN: 67904

Other (OTH) AF: 0.341 AC: 719 AN: 2110

Alfa AF: 0.355 Hom.: 1229

Bravo AF: 0.380

Asia WGS AF: 0.145 AC: 508 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	0.85
DANN	Benign	0.35
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6859237; hg19: chr5-76961;