10-57335928-G-A

Variant names:

• chr10-57335928-G-A
• rs12256364
• XR_001747453.1:n.483+9053C>T

Variant summary

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

The XR_001747453.1(LOC105378313):​n.483+9053C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,148 control chromosomes in the GnomAD database, including 3,709 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 0.16 (3709 hom., cov: 33)
• Consequence: LOC105378313 XR_001747453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 4 publications found

Genes affected

LOC105378313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837137.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308896	ENST00000837137.1		n.*51C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23930 AN: 152026 Hom.: 3698 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.158 AC: 23995 AN: 152148 Hom.: 3709 Cov.: 33 AF XY: 0.158 AC XY: 11756 AN XY: 74378

African (AFR) AF: 0.395 AC: 16398 AN: 41464

American (AMR) AF: 0.207 AC: 3170 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 157 AN: 3470

East Asian (EAS) AF: 0.0936 AC: 483 AN: 5158

South Asian (SAS) AF: 0.0850 AC: 410 AN: 4826

European-Finnish (FIN) AF: 0.0292 AC: 310 AN: 10608

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0401 AC: 2727 AN: 68024

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.0595 Hom.: 396

Bravo AF: 0.182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.20
DANN	Benign	0.65
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs12256364; hg19: chr10-59095688;