chr5-166891185-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377706	XR_941182.1	n.73+4468T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298538	ENST00000756290.1	n.146+8790A>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs3853240; hg19: chr5-166318190;