rs2502521

Variant names:

• chr6-74699718-T-C
• rs2502521
• ENST00000432484.6:n.199+34363A>G

Variant summary

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

The ENST00000432484.6(ENSG00000272243):​n.199+34363A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,976 control chromosomes in the GnomAD database, including 20,075 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 0.47 (20075 hom., cov: 32)
• Consequence: ENSG00000272243 ENST00000432484.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 2 publications found

Genes affected

ENSG00000272243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432484.6. 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
	LOC105377858	NR_187974.1		n.285+34363A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272243	ENST00000432484.6	TSL:3	n.199+34363A>G		intron	N/A
	ENSG00000272243	ENST00000658108.2		n.323+34363A>G		intron	N/A
	ENSG00000272243	ENST00000668767.1		n.199+34363A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70980 AN: 151858 Hom.: 20031 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.468 AC: 71079 AN: 151976 Hom.: 20075 Cov.: 32 AF XY: 0.462 AC XY: 34291 AN XY: 74266

African (AFR) AF: 0.805 AC: 33381 AN: 41482

American (AMR) AF: 0.393 AC: 5986 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3466

East Asian (EAS) AF: 0.330 AC: 1704 AN: 5158

South Asian (SAS) AF: 0.255 AC: 1232 AN: 4822

European-Finnish (FIN) AF: 0.318 AC: 3363 AN: 10574

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22724 AN: 67932

Other (OTH) AF: 0.444 AC: 934 AN: 2104

Alfa AF: 0.373 Hom.: 48599

Bravo AF: 0.488

Asia WGS AF: 0.347 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.59
PhyloP100		-0.73

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2502521;

hg19: chr6-75409434;