rs342092

Variant names:

• chr2-20498165-T-C
• rs342092
• ENST00000448241.2:n.690T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448241.2(ENSG00000228950):​n.690T>C 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 0.261 in 152,200 control chromosomes in the GnomAD database, including 5,450 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 0.26 (5450 hom., cov: 33)
• Consequence: ENSG00000228950 ENST00000448241.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 7 publications found

Genes affected

ENSG00000228950 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448241.2. 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
	LOC107985856	NR_157978.1		n.359+3001A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228950	ENST00000448241.2	TSL:4	n.690T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39634 AN: 152082 Hom.: 5454 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.261 AC: 39652 AN: 152200 Hom.: 5450 Cov.: 33 AF XY: 0.258 AC XY: 19181 AN XY: 74402

African (AFR) AF: 0.236 AC: 9782 AN: 41532

American (AMR) AF: 0.188 AC: 2883 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3468

East Asian (EAS) AF: 0.0549 AC: 285 AN: 5190

South Asian (SAS) AF: 0.204 AC: 983 AN: 4828

European-Finnish (FIN) AF: 0.318 AC: 3363 AN: 10576

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20555 AN: 67994

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.285 Hom.: 10264

Bravo AF: 0.250

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.76
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs342092; hg19: chr2-20697925;