rs2281854

Variant names:

• chr10-3227125-C-T
• rs2281854
• ENST00000445932.1:n.315C>T

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000236968 ENST00000445932.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 3 publications found

Genes affected

ENSG00000236968 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445932.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236968	ENST00000445932.1	TSL:2	n.315C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000236968	ENST00000732748.1		n.326C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000236968	ENST00000732749.1		n.409C>T		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0721 AC: 2990 AN: 41490

American (AMR) AF: 0.290 AC: 4434 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3472

East Asian (EAS) AF: 0.416 AC: 2132 AN: 5130

South Asian (SAS) AF: 0.475 AC: 2285 AN: 4814

European-Finnish (FIN) AF: 0.484 AC: 5111 AN: 10560

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24752 AN: 67962

Other (OTH) AF: 0.289 AC: 609 AN: 2110

Alfa AF: 0.354 Hom.: 5208

Bravo AF: 0.261

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.17
DANN	Benign	0.51
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2281854;

hg19: chr10-3269317;