2-62332070-T-C

Variant summary

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

The ENST00000689590.1(ENSG00000228541):n.163+35624T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,278 control chromosomes in the GnomAD database, including 25,981 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 0.58 (25981 hom., cov: 27)
• Consequence: ENST00000689590.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689590.1	n.163+35624T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.581 AC: 87820 AN: 151160 Hom.: 25954 Cov.: 27

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.581 AC: 87909 AN: 151278 Hom.: 25981 Cov.: 27 AF XY: 0.584 AC XY: 43188 AN XY: 73904

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.572

Alfa AF: 0.610 Hom.: 3547

Bravo AF: 0.570

Asia WGS AF: 0.618 AC: 2151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.35
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6759003; hg19: chr2-62559205;