ENST00000519555.1:n.250+7720T>C

Variant names:

• chr8-6092608-A-G
• rs752045
• ENST00000519555.1:n.250+7720T>C

Variant summary

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

The ENST00000519555.1(ENSG00000253880):​n.250+7720T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,210 control chromosomes in the GnomAD database, including 3,322 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 0.20 (3322 hom., cov: 33)
• Consequence: ENSG00000253880 ENST00000519555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 7 publications found

Genes affected

ENSG00000253880 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519555.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253880	ENST00000519555.1	TSL:4	n.250+7720T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30170 AN: 152090 Hom.: 3309 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.199 AC: 30232 AN: 152210 Hom.: 3322 Cov.: 33 AF XY: 0.200 AC XY: 14859 AN XY: 74424

African (AFR) AF: 0.269 AC: 11165 AN: 41512

American (AMR) AF: 0.210 AC: 3210 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3470

East Asian (EAS) AF: 0.173 AC: 897 AN: 5178

South Asian (SAS) AF: 0.258 AC: 1244 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1299 AN: 10604

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11014 AN: 68002

Other (OTH) AF: 0.193 AC: 408 AN: 2114

Alfa AF: 0.180 Hom.: 536

Bravo AF: 0.204

Asia WGS AF: 0.258 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.49
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs752045; hg19: chr8-5950130;