rs342115

Variant names:

• chr2-20465960-A-C
• rs342115
• ENST00000448241.2:n.308+13013A>C

Variant summary

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

The ENST00000448241.2(ENSG00000228950):​n.308+13013A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 152,280 control chromosomes in the GnomAD database, including 1,071 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 0.075 (1071 hom., cov: 33)
• Consequence: ENSG00000228950 ENST00000448241.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 2 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228950	ENST00000448241.2	TSL:4	n.308+13013A>C		intron	N/A
	ENSG00000228950	ENST00000838981.1		n.667+8368A>C		intron	N/A
	ENSG00000228950	ENST00000838982.1		n.559+8368A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11323 AN: 152162 Hom.: 1070 Cov.: 33

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0443

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00932

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0745 AC: 11352 AN: 152280 Hom.: 1071 Cov.: 33 AF XY: 0.0737 AC XY: 5488 AN XY: 74474

African (AFR) AF: 0.220 AC: 9120 AN: 41520

American (AMR) AF: 0.0442 AC: 677 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00912 AC: 44 AN: 4822

European-Finnish (FIN) AF: 0.0181 AC: 192 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0168 AC: 1141 AN: 68034

Other (OTH) AF: 0.0610 AC: 129 AN: 2116

Alfa AF: 0.0607 Hom.: 98

Bravo AF: 0.0833

Asia WGS AF: 0.0180 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.72
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs342115; hg19: chr2-20665721;