rs342070

Variant names:

• chr2-20485710-C-T
• rs342070
• ENST00000448241.2:n.309-12074C>T

Variant summary

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

The ENST00000448241.2(ENSG00000228950):​n.309-12074C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,070 control chromosomes in the GnomAD database, including 39,967 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 0.72 (39967 hom., cov: 32)
• Consequence: ENSG00000228950 ENST00000448241.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985856	NR_157978.1	n.530+3028G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228950	ENST00000448241.2	n.309-12074C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109582 AN: 151952 Hom.: 39946 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.721 AC: 109646 AN: 152070 Hom.: 39967 Cov.: 32 AF XY: 0.715 AC XY: 53191 AN XY: 74346

African (AFR) AF: 0.749 AC: 31043 AN: 41468

American (AMR) AF: 0.697 AC: 10650 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2509 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1950 AN: 5162

South Asian (SAS) AF: 0.552 AC: 2656 AN: 4810

European-Finnish (FIN) AF: 0.748 AC: 7913 AN: 10576

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50422 AN: 67980

Other (OTH) AF: 0.734 AC: 1547 AN: 2108

Alfa AF: 0.732 Hom.: 128148

Bravo AF: 0.719

Asia WGS AF: 0.500 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.57
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs342070; hg19: chr2-20685471;