rs2343278

Variant names:

• chr1-162968913-G-T
• rs2343278
• ENST00000798367.1:n.220-285C>A

Variant summary

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

The ENST00000798367.1(ENSG00000303955):​n.220-285C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,018 control chromosomes in the GnomAD database, including 36,200 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 0.69 (36200 hom., cov: 31)
• Consequence: ENSG00000303955 ENST00000798367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 2 publications found

Genes affected

ENSG00000303955 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303955	ENST00000798367.1	n.220-285C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104171 AN: 151900 Hom.: 36135 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.686 AC: 104302 AN: 152018 Hom.: 36200 Cov.: 31 AF XY: 0.685 AC XY: 50894 AN XY: 74280

African (AFR) AF: 0.785 AC: 32572 AN: 41480

American (AMR) AF: 0.718 AC: 10975 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1977 AN: 3472

East Asian (EAS) AF: 0.719 AC: 3701 AN: 5148

South Asian (SAS) AF: 0.527 AC: 2534 AN: 4812

European-Finnish (FIN) AF: 0.626 AC: 6602 AN: 10554

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43681 AN: 67954

Other (OTH) AF: 0.688 AC: 1454 AN: 2112

Alfa AF: 0.661 Hom.: 113719

Bravo AF: 0.700

Asia WGS AF: 0.651 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.058
DANN	Benign	0.31
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2343278; hg19: chr1-162938703;