rs1420846

Variant names:

• chr8-5278271-G-A
• rs1420846
• ENST00000778535.1:n.123+10510C>T

Variant summary

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

The ENST00000778535.1(ENSG00000301371):​n.123+10510C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,242 control chromosomes in the GnomAD database, including 55,929 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 0.86 (55929 hom., cov: 34)
• Consequence: ENSG00000301371 ENST00000778535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 1 publications found

Genes affected

ENSG00000301371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.897 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
ENSG00000301371	ENST00000778535.1	n.123+10510C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130243 AN: 152124 Hom.: 55896 Cov.: 34

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.856 AC: 130332 AN: 152242 Hom.: 55929 Cov.: 34 AF XY: 0.858 AC XY: 63871 AN XY: 74436

African (AFR) AF: 0.794 AC: 32994 AN: 41534

American (AMR) AF: 0.906 AC: 13848 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2886 AN: 3472

East Asian (EAS) AF: 0.918 AC: 4751 AN: 5174

South Asian (SAS) AF: 0.919 AC: 4442 AN: 4832

European-Finnish (FIN) AF: 0.864 AC: 9149 AN: 10586

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.872 AC: 59324 AN: 68032

Other (OTH) AF: 0.868 AC: 1834 AN: 2114

Alfa AF: 0.865 Hom.: 26932

Bravo AF: 0.857

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.60
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1420846; hg19: chr8-5135793;