rs17669878

Positions:

• chr10-100339816-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429420.1(ENSG00000231188):​n.212-2778C>G variant causes a intron, non coding transcript 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: ENST00000429420.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000429420.1	n.212-2778C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.351

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17669878; hg19: chr10-102099573;