ENST00000670247.2:n.326+11704C>G

Variant names:

• chr10-30541546-C-G
• rs3124177
• ENST00000670247.2:n.326+11704C>G

Variant summary

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

The ENST00000670247.2(ENSG00000287420):​n.326+11704C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,030 control chromosomes in the GnomAD database, including 7,495 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 0.31 (7495 hom., cov: 33)
• Consequence: ENSG00000287420 ENST00000670247.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892
• Publications: 0 publications found

Genes affected

ENSG00000287420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376478	XR_007062102.1	n.180+11704C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287420	ENST00000670247.2	n.326+11704C>G		intron_variant	Intron 1 of 1
ENSG00000287420	ENST00000844209.1	n.288+11704C>G		intron_variant	Intron 1 of 1
ENSG00000287420	ENST00000844210.1	n.190+11704C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47588 AN: 151912 Hom.: 7484 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.313 AC: 47627 AN: 152030 Hom.: 7495 Cov.: 33 AF XY: 0.315 AC XY: 23428 AN XY: 74296

African (AFR) AF: 0.331 AC: 13737 AN: 41480

American (AMR) AF: 0.317 AC: 4845 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1590 AN: 5160

South Asian (SAS) AF: 0.315 AC: 1516 AN: 4812

European-Finnish (FIN) AF: 0.339 AC: 3573 AN: 10548

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20402 AN: 67962

Other (OTH) AF: 0.314 AC: 664 AN: 2112

Alfa AF: 0.171 Hom.: 338

Bravo AF: 0.311

Asia WGS AF: 0.296 AC: 1031 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.40
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs3124177; hg19: chr10-30830475;