3-106475884-A-G

Variant names:

• chr3-106475884-A-G
• rs2953046
• ENST00000668075.2:n.210+24833T>C

Variant summary

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

The ENST00000668075.2(ENSG00000291293):​n.210+24833T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,832 control chromosomes in the GnomAD database, including 9,213 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 0.33 (9213 hom., cov: 32)
• Consequence: ENSG00000291293 ENST00000668075.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 1 publications found

Genes affected

ENSG00000291293 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929485	XR_007095992.1	n.1049+24833T>C		intron_variant	Intron 5 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291293	ENST00000668075.2	n.210+24833T>C		intron_variant	Intron 2 of 2
ENSG00000291293	ENST00000836909.1	n.97+24833T>C		intron_variant	Intron 1 of 3
ENSG00000291293	ENST00000836910.1	n.100+24833T>C		intron_variant	Intron 1 of 4
ENSG00000291293	ENST00000836911.1	n.185+9274T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49392 AN: 151714 Hom.: 9195 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.326 AC: 49448 AN: 151832 Hom.: 9213 Cov.: 32 AF XY: 0.328 AC XY: 24346 AN XY: 74192

African (AFR) AF: 0.468 AC: 19410 AN: 41448

American (AMR) AF: 0.370 AC: 5642 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3468

East Asian (EAS) AF: 0.639 AC: 3298 AN: 5164

South Asian (SAS) AF: 0.398 AC: 1916 AN: 4820

European-Finnish (FIN) AF: 0.187 AC: 1974 AN: 10566

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15335 AN: 67812

Other (OTH) AF: 0.333 AC: 701 AN: 2108

Alfa AF: 0.231 Hom.: 2194

Bravo AF: 0.348

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.23
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2953046; hg19: chr3-106194731;