rs2203858

Variant names:

• chr15-21293860-T-C
• rs2203858
• ENST00000556425.2:n.1342A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000556425.2(ENSG00000237161):​n.1342A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.30 (2 hom., cov: 0)
  • Exomes 𝑓: 0.34 (34 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000237161 ENST00000556425.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 2 publications found

Genes affected

ENSG00000237161 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556425.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC646214	NR_027053.2		n.3970A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237161	ENST00000556425.2	TSL:6	n.1342A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000295468	ENST00000730279.1		n.424-2123A>G		intron	N/A
	ENSG00000295468	ENST00000730280.1		n.424-2161A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.302 AC: 697 AN: 2306 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.273

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.342 AC: 25257 AN: 73746 Hom.: 34 Cov.: 0 AF XY: 0.343 AC XY: 12844 AN XY: 37500

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.336 AC: 808 AN: 2402

American (AMR) AF: 0.299 AC: 643 AN: 2150

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 927 AN: 2910

East Asian (EAS) AF: 0.383 AC: 2543 AN: 6648

South Asian (SAS) AF: 0.332 AC: 434 AN: 1308

European-Finnish (FIN) AF: 0.401 AC: 1894 AN: 4728

Middle Eastern (MID) AF: 0.295 AC: 109 AN: 370

European-Non Finnish (NFE) AF: 0.336 AC: 16191 AN: 48194

Other (OTH) AF: 0.339 AC: 1708 AN: 5036

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.303 AC: 695 AN: 2292 Hom.: 2 Cov.: 0 AF XY: 0.296 AC XY: 302 AN XY: 1020

African (AFR) AF: 0.303 AC: 122 AN: 402

American (AMR) AF: 0.231 AC: 50 AN: 216

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 17 AN: 64

East Asian (EAS) AF: 0.318 AC: 70 AN: 220

South Asian (SAS) AF: 0.291 AC: 43 AN: 148

European-Finnish (FIN) AF: 0.367 AC: 11 AN: 30

Middle Eastern (MID) AF: 0.167 AC: 3 AN: 18

European-Non Finnish (NFE) AF: 0.319 AC: 365 AN: 1144

Other (OTH) AF: 0.273 AC: 12 AN: 44

Alfa AF: 0.251 Hom.: 38

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	18
DANN	Benign	0.63
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2203858; hg19: chr15-21936770; COSMIC: COSV70888071;