rs735877

Positions:

• chr10-100344764-C-T

Variant summary

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

The ENST00000429420.1(ENSG00000231188):​n.103+1524G>A 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 0.41 in 501,206 control chromosomes in the GnomAD database, including 44,382 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 0.45 (16291 hom., cov: 32)
  • Exomes 𝑓: 0.39 (28091 hom.)
• Consequence: ENST00000429420.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000429420.1	n.103+1524G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68592 AN: 151692 Hom.: 16275 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.435

GnomAD3 exomes AF: 0.393 AC: 86185 AN: 219426 Hom.: 17676 AF XY: 0.397 AC XY: 48175 AN XY: 121404

Gnomad AFR exome AF: 0.599

Gnomad AMR exome AF: 0.312

Gnomad ASJ exome AF: 0.337

Gnomad EAS exome AF: 0.347

Gnomad SAS exome AF: 0.453

Gnomad FIN exome AF: 0.458

Gnomad NFE exome AF: 0.381

Gnomad OTH exome AF: 0.384

GnomAD4 exome AF: 0.392 AC: 137027 AN: 349396 Hom.: 28091 Cov.: 0 AF XY: 0.399 AC XY: 79972 AN XY: 200478

Gnomad4 AFR exome AF: 0.586

Gnomad4 AMR exome AF: 0.317

Gnomad4 ASJ exome AF: 0.331

Gnomad4 EAS exome AF: 0.339

Gnomad4 SAS exome AF: 0.452

Gnomad4 FIN exome AF: 0.445

Gnomad4 NFE exome AF: 0.378

Gnomad4 OTH exome AF: 0.396

GnomAD4 genome AF: 0.452 AC: 68653 AN: 151810 Hom.: 16291 Cov.: 32 AF XY: 0.457 AC XY: 33883 AN XY: 74178

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.435

Alfa AF: 0.391 Hom.: 28562

Bravo AF: 0.447

Asia WGS AF: 0.438 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735877; hg19: chr10-102104521; COSMIC: COSV64853471;