5-82963236-G-T

Variant names:

• chr5-82963236-G-T
• rs379857
• ENST00000504916.2:n.416+12108C>A

Variant summary

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

The ENST00000504916.2(ENSG00000248112):​n.416+12108C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,956 control chromosomes in the GnomAD database, including 20,331 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 0.50 (20331 hom., cov: 32)
• Consequence: ENSG00000248112 ENST00000504916.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 3 publications found

Genes affected

ENSG00000248112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504916.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105379051	NR_188290.1		n.373+12108C>A		intron	N/A
	LOC105379051	NR_188291.1		n.373+12108C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248112	ENST00000504916.2	TSL:3	n.416+12108C>A		intron	N/A
	ENSG00000248112	ENST00000718043.1		n.553+8821C>A		intron	N/A
	ENSG00000248112	ENST00000718044.1		n.407+12108C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76590 AN: 151836 Hom.: 20318 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.504 AC: 76654 AN: 151956 Hom.: 20331 Cov.: 32 AF XY: 0.504 AC XY: 37466 AN XY: 74286

African (AFR) AF: 0.628 AC: 26032 AN: 41438

American (AMR) AF: 0.543 AC: 8280 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1883 AN: 3468

East Asian (EAS) AF: 0.828 AC: 4280 AN: 5168

South Asian (SAS) AF: 0.463 AC: 2229 AN: 4816

European-Finnish (FIN) AF: 0.329 AC: 3479 AN: 10564

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28741 AN: 67936

Other (OTH) AF: 0.523 AC: 1103 AN: 2108

Alfa AF: 0.470 Hom.: 3104

Bravo AF: 0.533

Asia WGS AF: 0.581 AC: 2017 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.57
DANN	Benign	0.37
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs379857; hg19: chr5-82259055;