5-35851159-G-T

Variant names:

• chr5-35851159-G-T
• rs12516866
• ENST00000736912.1:n.55+3161C>A

Variant summary

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

The ENST00000736912.1(ENSG00000248969):​n.55+3161C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,966 control chromosomes in the GnomAD database, including 12,052 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 0.40 (12052 hom., cov: 32)
• Consequence: ENSG00000248969 ENST00000736912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.863
• Publications: 14 publications found

Genes affected

ENSG00000248969 (HGNC:59028):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736912.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248969	ENST00000736912.1		n.55+3161C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60298 AN: 151850 Hom.: 12052 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.397 AC: 60320 AN: 151966 Hom.: 12052 Cov.: 32 AF XY: 0.397 AC XY: 29455 AN XY: 74260

African (AFR) AF: 0.391 AC: 16205 AN: 41422

American (AMR) AF: 0.342 AC: 5222 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3468

East Asian (EAS) AF: 0.426 AC: 2198 AN: 5154

South Asian (SAS) AF: 0.350 AC: 1687 AN: 4816

European-Finnish (FIN) AF: 0.453 AC: 4784 AN: 10564

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27559 AN: 67966

Other (OTH) AF: 0.378 AC: 796 AN: 2108

Alfa AF: 0.397 Hom.: 1768

Bravo AF: 0.393

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.3
DANN	Benign	0.27
PhyloP100		0.86

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12516866;

hg19: chr5-35851261;