5-166891185-A-G

Variant names:

• chr5-166891185-A-G
• rs3853240
• ENST00000756290.1:n.146+8790A>G

Variant summary

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

The ENST00000756290.1(ENSG00000298538):​n.146+8790A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0826 in 152,290 control chromosomes in the GnomAD database, including 661 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 0.083 (661 hom., cov: 32)
• Consequence: ENSG00000298538 ENST00000756290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 2 publications found

Genes affected

ENSG00000298538 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756290.1. 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
	ENSG00000298538	ENST00000756290.1		n.146+8790A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0825 AC: 12557 AN: 152172 Hom.: 656 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0796

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0826 AC: 12583 AN: 152290 Hom.: 661 Cov.: 32 AF XY: 0.0813 AC XY: 6056 AN XY: 74478

African (AFR) AF: 0.148 AC: 6137 AN: 41554

American (AMR) AF: 0.0795 AC: 1216 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3470

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5182

South Asian (SAS) AF: 0.0899 AC: 434 AN: 4828

European-Finnish (FIN) AF: 0.0231 AC: 245 AN: 10624

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0605 AC: 4117 AN: 68022

Other (OTH) AF: 0.0823 AC: 174 AN: 2114

Alfa AF: 0.0690 Hom.: 929

Bravo AF: 0.0893

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.32
PhyloP100		-0.15

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: rs3853240;

hg19: chr5-166318190;