chr2-20496496-G-T

Variant names:

• chr2-20496496-G-T
• rs342096
• ENST00000448241.2:n.309-1288G>T

Variant summary

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

The ENST00000448241.2(ENSG00000228950):​n.309-1288G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,150 control chromosomes in the GnomAD database, including 5,343 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 (5343 hom., cov: 32)
• Consequence: ENSG00000228950 ENST00000448241.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.912
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC107985856	NR_157978.1		n.359+4670C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228950	ENST00000448241.2	TSL:4	n.309-1288G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39234 AN: 152032 Hom.: 5348 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.258 AC: 39245 AN: 152150 Hom.: 5343 Cov.: 32 AF XY: 0.255 AC XY: 18985 AN XY: 74380

African (AFR) AF: 0.233 AC: 9692 AN: 41534

American (AMR) AF: 0.186 AC: 2847 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3470

East Asian (EAS) AF: 0.0546 AC: 283 AN: 5186

South Asian (SAS) AF: 0.201 AC: 968 AN: 4818

European-Finnish (FIN) AF: 0.318 AC: 3363 AN: 10586

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20311 AN: 67956

Other (OTH) AF: 0.242 AC: 509 AN: 2106

Alfa AF: 0.282 Hom.: 21916

Bravo AF: 0.247

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.0
DANN	Benign	0.87
PhyloP100		0.91

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: rs342096;

hg19: chr2-20696256;