rs17669878

Variant names:

• chr10-100339816-G-C
• rs17669878
• ENST00000429420.1:n.212-2778C>G

Variant summary

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

The ENST00000429420.1(ENSG00000231188):​n.212-2778C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,186 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: 33)
• Consequence: ENSG00000231188 ENST00000429420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 5 publications found

Genes affected

ENSG00000231188 (HGNC:58401):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429420.1. 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
	ENSG00000231188	ENST00000429420.1	TSL:3	n.212-2778C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50648 AN: 152068 Hom.: 9220 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.333 AC: 50638 AN: 152186 Hom.: 9213 Cov.: 33 AF XY: 0.340 AC XY: 25316 AN XY: 74396

African (AFR) AF: 0.182 AC: 7576 AN: 41538

American (AMR) AF: 0.345 AC: 5277 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3464

East Asian (EAS) AF: 0.310 AC: 1605 AN: 5176

South Asian (SAS) AF: 0.420 AC: 2029 AN: 4830

European-Finnish (FIN) AF: 0.458 AC: 4848 AN: 10574

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26726 AN: 68006

Other (OTH) AF: 0.351 AC: 741 AN: 2112

Alfa AF: 0.364 Hom.: 1327

Bravo AF: 0.314

Asia WGS AF: 0.346 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.64
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs17669878; hg19: chr10-102099573;