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. Variant got -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

Genes affected

ENSG00000286136 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.946

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.804

Alfa AF: 0.809 Hom.: 9177

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2851365; hg19: chr4-109596447;