rs7527580

Variant names:

• chr1-19052014-G-A
• rs7527580
• ENST00000823875.1:n.112+3053C>T

Variant summary

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

The ENST00000823875.1(ENSG00000307102):​n.112+3053C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 152,114 control chromosomes in the GnomAD database, including 144 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 0.035 (144 hom., cov: 31)
• Consequence: ENSG00000307102 ENST00000823875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 1 publications found

Genes affected

ENSG00000307102 (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 = 0.102 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
ENSG00000307102	ENST00000823875.1	n.112+3053C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0347 AC: 5267 AN: 151996 Hom.: 145 Cov.: 31

Gnomad AFR AF: 0.00855

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0304

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0346 AC: 5264 AN: 152114 Hom.: 144 Cov.: 31 AF XY: 0.0348 AC XY: 2587 AN XY: 74346

African (AFR) AF: 0.00853 AC: 354 AN: 41524

American (AMR) AF: 0.0304 AC: 465 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3468

East Asian (EAS) AF: 0.110 AC: 568 AN: 5168

South Asian (SAS) AF: 0.0643 AC: 309 AN: 4808

European-Finnish (FIN) AF: 0.0544 AC: 575 AN: 10578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0428 AC: 2910 AN: 67982

Other (OTH) AF: 0.0237 AC: 50 AN: 2108

Alfa AF: 0.0402 Hom.: 418

Bravo AF: 0.0322

Asia WGS AF: 0.0830 AC: 286 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	0.039
DANN	Benign	0.62
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs7527580; hg19: chr1-19378508;