rs6870861

Variant names:

• chr5-131097262-C-G
• rs6870861
• ENST00000840920.1:n.487-12529C>G

Variant summary

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

The ENST00000840920.1(ENSG00000309416):​n.487-12529C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,258 control chromosomes in the GnomAD database, including 61,736 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 0.90 (61736 hom., cov: 32)
• Consequence: ENSG00000309416 ENST00000840920.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 4 publications found

Genes affected

ENSG00000309416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 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
ENSG00000309416	ENST00000840920.1	n.487-12529C>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136724 AN: 152140 Hom.: 61670 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.899 AC: 136849 AN: 152258 Hom.: 61736 Cov.: 32 AF XY: 0.896 AC XY: 66659 AN XY: 74420

African (AFR) AF: 0.961 AC: 39925 AN: 41566

American (AMR) AF: 0.933 AC: 14277 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2989 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4128 AN: 5180

South Asian (SAS) AF: 0.907 AC: 4379 AN: 4826

European-Finnish (FIN) AF: 0.786 AC: 8313 AN: 10582

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59861 AN: 68014

Other (OTH) AF: 0.902 AC: 1904 AN: 2112

Alfa AF: 0.890 Hom.: 7577

Bravo AF: 0.912

Asia WGS AF: 0.884 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
DANN	Benign	0.41
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs6870861; hg19: chr5-130432955;