rs2851365

Variant names:

• chr4-108675291-G-A
• rs2851365
• ENST00000651728.2:n.232-2505G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-108675291-G-A
• chr4-108675291-G-C
• chr4-108675291-G-T

Variant summary

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

The ENST00000651728.2(ENSG00000286136):​n.232-2505G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,134 control chromosomes in the GnomAD database, including 50,665 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 0.81 (50665 hom., cov: 32)
• Consequence: ENSG00000286136 ENST00000651728.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 2 publications found

Genes affected

ENSG00000286136 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000286136	ENST00000651728.2	n.232-2505G>A		intron_variant	Intron 2 of 2
ENSG00000286136	ENST00000810390.1	n.284-2505G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123646 AN: 152016 Hom.: 50616 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.813 AC: 123750 AN: 152134 Hom.: 50665 Cov.: 32 AF XY: 0.813 AC XY: 60480 AN XY: 74348

African (AFR) AF: 0.857 AC: 35566 AN: 41524

American (AMR) AF: 0.857 AC: 13102 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2766 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5172 AN: 5176

South Asian (SAS) AF: 0.946 AC: 4565 AN: 4828

European-Finnish (FIN) AF: 0.653 AC: 6888 AN: 10550

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.781 AC: 53088 AN: 67982

Other (OTH) AF: 0.804 AC: 1694 AN: 2108

Alfa AF: 0.810 Hom.: 9458

Bravo AF: 0.830

Asia WGS AF: 0.957 AC: 3324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.37
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2851365; hg19: chr4-109596447;