10-100344764-C-T

Variant names:

• chr10-100344764-C-T
• rs735877
• ENST00000429420.1:n.103+1524G>A

Variant summary

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

The ENST00000429420.1(ENSG00000231188):​n.103+1524G>A variant causes a intron 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: ENSG00000231188 ENST00000429420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 20 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231188	ENST00000429420.1	TSL:3	n.103+1524G>A		intron	N/A

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

GnomAD2 exomes AF: 0.393 AC: 86185 AN: 219426 AF XY: 0.397

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 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

African (AFR) AF: 0.586 AC: 5652 AN: 9640

American (AMR) AF: 0.317 AC: 10973 AN: 34642

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 3756 AN: 11332

East Asian (EAS) AF: 0.339 AC: 4332 AN: 12782

South Asian (SAS) AF: 0.452 AC: 28141 AN: 62226

European-Finnish (FIN) AF: 0.445 AC: 7278 AN: 16352

Middle Eastern (MID) AF: 0.383 AC: 1063 AN: 2778

European-Non Finnish (NFE) AF: 0.378 AC: 69544 AN: 183772

Other (OTH) AF: 0.396 AC: 6288 AN: 15872

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

African (AFR) AF: 0.607 AC: 25113 AN: 41386

American (AMR) AF: 0.382 AC: 5834 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1188 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1975 AN: 5170

South Asian (SAS) AF: 0.467 AC: 2247 AN: 4814

European-Finnish (FIN) AF: 0.460 AC: 4815 AN: 10470

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26015 AN: 67910

Other (OTH) AF: 0.435 AC: 919 AN: 2114

Alfa AF: 0.400 Hom.: 59545

Bravo AF: 0.447

Asia WGS AF: 0.438 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.61
PhyloP100		-1.3

Splicing

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

Other links and lift over

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