rs880253

chr2-190764960-C-T

Variant summary

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

The ENST00000676095.2(ENSG00000228509):n.195-25629G>A 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 0.106 in 152,108 control chromosomes in the GnomAD database, including 1,430 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 0.11 (1430 hom., cov: 33)
• Consequence: ENST00000676095.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 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
	ENST00000676095.2	n.195-25629G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16036 AN: 151990 Hom.: 1421 Cov.: 33

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0435

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.106 AC: 16068 AN: 152108 Hom.: 1430 Cov.: 33 AF XY: 0.111 AC XY: 8250 AN XY: 74368

Gnomad4 AFR AF: 0.0853

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.0435

Gnomad4 NFE AF: 0.0651

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0859 Hom.: 409

Bravo AF: 0.125

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	12
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs880253; hg19: chr2-191629686;