rs7528615

Variant names:

• chr1-84267280-T-C
• rs7528615
• ENST00000721911.1:n.745-13002A>G

Variant summary

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

The ENST00000721911.1(ENSG00000294213):​n.745-13002A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,024 control chromosomes in the GnomAD database, including 7,758 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 0.29 (7758 hom., cov: 31)
• Consequence: ENSG00000294213 ENST00000721911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 7 publications found

Genes affected

ENSG00000294213 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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
ENSG00000294213	ENST00000721911.1	n.745-13002A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43686 AN: 151906 Hom.: 7757 Cov.: 31

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.287 AC: 43681 AN: 152024 Hom.: 7758 Cov.: 31 AF XY: 0.290 AC XY: 21573 AN XY: 74302

African (AFR) AF: 0.0826 AC: 3427 AN: 41476

American (AMR) AF: 0.317 AC: 4838 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3466

East Asian (EAS) AF: 0.623 AC: 3208 AN: 5152

South Asian (SAS) AF: 0.494 AC: 2372 AN: 4806

European-Finnish (FIN) AF: 0.314 AC: 3317 AN: 10566

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24821 AN: 67964

Other (OTH) AF: 0.269 AC: 566 AN: 2108

Alfa AF: 0.338 Hom.: 17807

Bravo AF: 0.276

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.69
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7528615; hg19: chr1-84732963; COSMIC: COSV59966922;