ENST00000668075.2:n.210+19608A>G

Variant names:

• chr3-106481109-T-C
• rs2712464
• ENST00000668075.2:n.210+19608A>G

Variant summary

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

The ENST00000668075.2(ENSG00000291293):​n.210+19608A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,912 control chromosomes in the GnomAD database, including 8,695 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 0.32 (8695 hom., cov: 32)
• Consequence: ENSG00000291293 ENST00000668075.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929485	XR_007095992.1	n.1049+19608A>G		intron_variant	Intron 5 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291293	ENST00000668075.2	n.210+19608A>G		intron_variant	Intron 2 of 2
ENSG00000291293	ENST00000836909.1	n.97+19608A>G		intron_variant	Intron 1 of 3
ENSG00000291293	ENST00000836910.1	n.100+19608A>G		intron_variant	Intron 1 of 4
ENSG00000291293	ENST00000836911.1	n.185+4049A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48477 AN: 151794 Hom.: 8677 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.319 AC: 48534 AN: 151912 Hom.: 8695 Cov.: 32 AF XY: 0.321 AC XY: 23840 AN XY: 74254

African (AFR) AF: 0.464 AC: 19217 AN: 41374

American (AMR) AF: 0.370 AC: 5641 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3472

East Asian (EAS) AF: 0.499 AC: 2576 AN: 5158

South Asian (SAS) AF: 0.389 AC: 1870 AN: 4806

European-Finnish (FIN) AF: 0.187 AC: 1976 AN: 10566

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

European-Non Finnish (NFE) AF: 0.226 AC: 15369 AN: 67958

Other (OTH) AF: 0.329 AC: 692 AN: 2106

Alfa AF: 0.254 Hom.: 7720

Bravo AF: 0.341

Asia WGS AF: 0.447 AC: 1554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.85
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2712464; hg19: chr3-106199956;