ENST00000690550.2:n.147-49601G>C

Variant names:

• chr10-57158352-C-G
• rs3107503
• ENST00000690550.2:n.147-49601G>C

Variant summary

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

The ENST00000690550.2(ENSG00000289158):​n.147-49601G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,588 control chromosomes in the GnomAD database, including 29,455 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 0.60 (29455 hom., cov: 30)
• Consequence: ENSG00000289158 ENST00000690550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 1 publications found

Genes affected

ENSG00000289158 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289158	ENST00000690550.2	n.147-49601G>C		intron_variant	Intron 1 of 2
ENSG00000289158	ENST00000752897.1	n.152-49601G>C		intron_variant	Intron 1 of 3
ENSG00000289158	ENST00000752899.1	n.67-18142G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 90959 AN: 151470 Hom.: 29448 Cov.: 30

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.600 AC: 90993 AN: 151588 Hom.: 29455 Cov.: 30 AF XY: 0.603 AC XY: 44656 AN XY: 74064

African (AFR) AF: 0.339 AC: 14004 AN: 41334

American (AMR) AF: 0.678 AC: 10314 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2789 AN: 3468

East Asian (EAS) AF: 0.869 AC: 4411 AN: 5078

South Asian (SAS) AF: 0.645 AC: 3102 AN: 4810

European-Finnish (FIN) AF: 0.672 AC: 7068 AN: 10518

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.697 AC: 47274 AN: 67850

Other (OTH) AF: 0.617 AC: 1304 AN: 2114

Alfa AF: 0.556 Hom.: 1845

Bravo AF: 0.588

Asia WGS AF: 0.693 AC: 2411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.76
DANN	Benign	0.69
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs3107503; hg19: chr10-58918112;