2-62380963-T-C

Variant names:

• chr2-62380963-T-C
• rs6715590
• ENST00000687402.2:n.196-27167T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687402.2(ENSG00000228541):​n.196-27167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,842 control chromosomes in the GnomAD database, including 11,442 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 0.35 (11442 hom., cov: 31)
• Consequence: ENSG00000228541 ENST00000687402.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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
ENSG00000228541	ENST00000687402.2	n.196-27167T>C		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000689590.1	n.164-82876T>C		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000701158.1	n.198-45271T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53648 AN: 151726 Hom.: 11398 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.354 AC: 53751 AN: 151842 Hom.: 11442 Cov.: 31 AF XY: 0.355 AC XY: 26384 AN XY: 74224

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.351

Alfa AF: 0.285 Hom.: 1714

Bravo AF: 0.378

Asia WGS AF: 0.531 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6715590; hg19: chr2-62608098;