chr3-3525677-C-A

Variant names:

• chr3-3525677-C-A
• rs10510269
• ENST00000420000.6:n.200+101067G>T

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.200+101067G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,114 control chromosomes in the GnomAD database, including 2,284 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 0.15 (2284 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223727	ENST00000420000.6	n.200+101067G>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22604 AN: 151996 Hom.: 2286 Cov.: 32

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.149 AC: 22599 AN: 152114 Hom.: 2284 Cov.: 32 AF XY: 0.146 AC XY: 10892 AN XY: 74366

Gnomad4 AFR AF: 0.0425

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.135

Alfa AF: 0.186 Hom.: 606

Bravo AF: 0.130

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.85
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510269; hg19: chr3-3567361;