rs7252525

Variant names:

• chr19-54298005-C-T
• rs7252525
• ENST00000733241.1:n.153+578G>A

Variant summary

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

The ENST00000733241.1(ENSG00000295857):​n.153+578G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0674 in 152,486 control chromosomes in the GnomAD database, including 395 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 0.067 (394 hom., cov: 32)
  • Exomes 𝑓: 0.048 (1 hom.)
• Consequence: ENSG00000295857 ENST00000733241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694
• Publications: 3 publications found

Genes affected

ENSG00000295857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0862 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733241.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295857	ENST00000733241.1		n.153+578G>A		intron	N/A
	ENSG00000295857	ENST00000733242.1		n.185+578G>A		intron	N/A
	ENSG00000251431	ENST00000514037.1	TSL:6	n.*100G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0675 AC: 10267 AN: 152158 Hom.: 393 Cov.: 32

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0762

GnomAD4 exome AF: 0.0476 AC: 10 AN: 210 Hom.: 1 Cov.: 0 AF XY: 0.0714 AC XY: 8 AN XY: 112

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.125 AC: 1 AN: 8

European-Finnish (FIN) AF: 0.0294 AC: 1 AN: 34

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0446 AC: 5 AN: 112

Other (OTH) AF: 0.0750 AC: 3 AN: 40

GnomAD4 genome AF: 0.0674 AC: 10263 AN: 152276 Hom.: 394 Cov.: 32 AF XY: 0.0675 AC XY: 5024 AN XY: 74454

African (AFR) AF: 0.0347 AC: 1440 AN: 41558

American (AMR) AF: 0.0573 AC: 876 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3472

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5182

South Asian (SAS) AF: 0.0706 AC: 341 AN: 4830

European-Finnish (FIN) AF: 0.0858 AC: 911 AN: 10618

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0881 AC: 5990 AN: 68004

Other (OTH) AF: 0.0750 AC: 158 AN: 2108

Alfa AF: 0.0826 Hom.: 787

Bravo AF: 0.0635

Asia WGS AF: 0.0400 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.71
PhyloP100		0.69
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7252525; hg19: chr19-54808614;