rs562843

Variant names:

• chr8-26870301-T-G
• rs562843
• ENST00000797227.1:n.124+4010T>G

Variant summary

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

The ENST00000797227.1(ENSG00000303788):​n.124+4010T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.91 in 152,212 control chromosomes in the GnomAD database, including 63,240 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 0.91 (63240 hom., cov: 31)
• Consequence: ENSG00000303788 ENST00000797227.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 1 publications found

Genes affected

ENSG00000303788 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 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
ENSG00000303788	ENST00000797227.1	n.124+4010T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.910 AC: 138387 AN: 152094 Hom.: 63204 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.910 AC: 138477 AN: 152212 Hom.: 63240 Cov.: 31 AF XY: 0.910 AC XY: 67751 AN XY: 74414

African (AFR) AF: 0.823 AC: 34167 AN: 41508

American (AMR) AF: 0.890 AC: 13608 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3433 AN: 3472

East Asian (EAS) AF: 0.909 AC: 4707 AN: 5180

South Asian (SAS) AF: 0.932 AC: 4486 AN: 4812

European-Finnish (FIN) AF: 0.942 AC: 9993 AN: 10606

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64995 AN: 68034

Other (OTH) AF: 0.907 AC: 1914 AN: 2110

Alfa AF: 0.927 Hom.: 8475

Bravo AF: 0.902

Asia WGS AF: 0.898 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.65
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs562843; hg19: chr8-26727818;