5-109998782-C-T

Variant names:

• chr5-109998782-C-T
• rs36784
• ENST00000812526.1:n.218-23108C>T

Variant summary

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

The ENST00000812526.1(ENSG00000305706):​n.218-23108C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.986 in 152,190 control chromosomes in the GnomAD database, including 73,984 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 0.99 (73984 hom., cov: 30)
• Consequence: ENSG00000305706 ENST00000812526.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 1 publications found

Genes affected

ENSG00000305706 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812526.1. 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
	ENSG00000305706	ENST00000812526.1		n.218-23108C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.986 AC: 149916 AN: 152072 Hom.: 73931 Cov.: 30

Gnomad AFR AF: 0.977

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.997

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.990

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.983

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

GnomAD4 genome AF: 0.986 AC: 150028 AN: 152190 Hom.: 73984 Cov.: 30 AF XY: 0.985 AC XY: 73317 AN XY: 74412

African (AFR) AF: 0.977 AC: 40573 AN: 41542

American (AMR) AF: 0.997 AC: 15206 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3470 AN: 3472

East Asian (EAS) AF: 0.898 AC: 4634 AN: 5158

South Asian (SAS) AF: 0.977 AC: 4713 AN: 4824

European-Finnish (FIN) AF: 0.990 AC: 10495 AN: 10606

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67654 AN: 68010

Other (OTH) AF: 0.982 AC: 2077 AN: 2116

Alfa AF: 0.993 Hom.: 49432

Bravo AF: 0.985

Asia WGS AF: 0.953 AC: 3310 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.8
DANN	Benign	0.38
PhyloP100		0.31

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: rs36784;

hg19: chr5-109334483;