rs2521030

Variant names:

• chr7-126229262-G-C
• rs2521030
• ENST00000809641.1:n.145-4275G>C

Variant summary

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

The ENST00000809641.1(ENSG00000305210):​n.145-4275G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,018 control chromosomes in the GnomAD database, including 5,576 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 0.26 (5576 hom., cov: 32)
• Consequence: ENSG00000305210 ENST00000809641.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 2 publications found

Genes affected

ENSG00000305210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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
ENSG00000305210	ENST00000809641.1	n.145-4275G>C		intron_variant	Intron 1 of 2
ENSG00000305210	ENST00000809642.1	n.-58G>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39075 AN: 151900 Hom.: 5572 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.257 AC: 39107 AN: 152018 Hom.: 5576 Cov.: 32 AF XY: 0.261 AC XY: 19359 AN XY: 74294

African (AFR) AF: 0.376 AC: 15579 AN: 41448

American (AMR) AF: 0.213 AC: 3248 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3470

East Asian (EAS) AF: 0.232 AC: 1197 AN: 5162

South Asian (SAS) AF: 0.171 AC: 826 AN: 4828

European-Finnish (FIN) AF: 0.347 AC: 3659 AN: 10558

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13171 AN: 67958

Other (OTH) AF: 0.235 AC: 497 AN: 2112

Alfa AF: 0.229 Hom.: 547

Bravo AF: 0.256

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.42
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2521030; hg19: chr7-125869316;