rs2303970

Positions:

• chr12-74077560-C-T

Variant summary

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

The variant allele was found at a frequency of 0.552 in 151,982 control chromosomes in the GnomAD database, including 24,792 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 0.55 (24792 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.74077560C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02882	ENST00000653134.1	n.777+73442G>A		intron_variant
LINC02882	ENST00000663261.1	n.709+73442G>A		intron_variant
LINC02882	ENST00000665907.1	n.636+73442G>A		intron_variant
LINC02882	ENST00000669556.1	n.570+73442G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83801 AN: 151864 Hom.: 24743 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.552 AC: 83905 AN: 151982 Hom.: 24792 Cov.: 32 AF XY: 0.547 AC XY: 40648 AN XY: 74280

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.499

Alfa AF: 0.478 Hom.: 36164

Bravo AF: 0.573

Asia WGS AF: 0.441 AC: 1531 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2303970; hg19: chr12-74471340;