rs2281854

Positions:

• chr10-3227125-C-T

Variant summary

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

The ENST00000445932.1(ENSG00000236968):​n.315C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,012 control chromosomes in the GnomAD database, including 8,056 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 0.29 (8056 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000445932.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 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
	ENST00000445932.1	n.315C>T		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43871 AN: 151892 Hom.: 8052 Cov.: 32

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.284

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.289 AC: 43885 AN: 152012 Hom.: 8056 Cov.: 32 AF XY: 0.299 AC XY: 22236 AN XY: 74306

Gnomad4 AFR AF: 0.0721

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.289

Alfa AF: 0.353 Hom.: 4706

Bravo AF: 0.261

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.17
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2281854; hg19: chr10-3269317;