rs2851365

chr4-108675291-G-Achr4-108675291-G-Cchr4-108675291-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, non coding transcript 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: ENST00000651728.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651728.2	n.232-2505G>A		intron_variant, non_coding_transcript_variant

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;