rs12103757

Variant names:

• chr17-70478692-A-G
• rs12103757
• ENST00000785193.1:n.477-23351A>G

Variant summary

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

The ENST00000785193.1(ENSG00000302248):​n.477-23351A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,018 control chromosomes in the GnomAD database, including 20,143 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 0.51 (20143 hom., cov: 32)
• Consequence: ENSG00000302248 ENST00000785193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 5 publications found

Genes affected

ENSG00000302248 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785193.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302248	ENST00000785193.1		n.477-23351A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77618 AN: 151900 Hom.: 20111 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.511 AC: 77708 AN: 152018 Hom.: 20143 Cov.: 32 AF XY: 0.509 AC XY: 37835 AN XY: 74300

African (AFR) AF: 0.492 AC: 20389 AN: 41440

American (AMR) AF: 0.554 AC: 8458 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2071 AN: 3470

East Asian (EAS) AF: 0.683 AC: 3530 AN: 5168

South Asian (SAS) AF: 0.593 AC: 2862 AN: 4824

European-Finnish (FIN) AF: 0.342 AC: 3613 AN: 10570

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34890 AN: 67962

Other (OTH) AF: 0.536 AC: 1134 AN: 2114

Alfa AF: 0.508 Hom.: 2554

Bravo AF: 0.527

Asia WGS AF: 0.679 AC: 2349 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0060
DANN	Benign	0.76
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12103757;

hg19: chr17-68474833;