rs3885668

Positions:

• chr2-10038352-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 0.6 in 152,082 control chromosomes in the GnomAD database, including 27,873 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 0.60 (27873 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10038352C>T		intergenic_region
LOC112268412	XR_002959369.2	n.1357-26C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91224 AN: 151964 Hom.: 27839 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.600 AC: 91310 AN: 152082 Hom.: 27873 Cov.: 32 AF XY: 0.611 AC XY: 45422 AN XY: 74340

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.594

Alfa AF: 0.586 Hom.: 11922

Bravo AF: 0.591

Asia WGS AF: 0.740 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.039
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3885668; hg19: chr2-10178479;