rs928565

chr10-44337436-G-Achr10-44337436-G-Cchr10-44337436-G-T

Variant summary

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

The XR_007062369.1(LOC124902544):n.3742+10112C>T 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 0.465 in 151,960 control chromosomes in the GnomAD database, including 17,235 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 0.46 (17235 hom., cov: 32)
• Consequence: LOC124902544 XR_007062369.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

Genes affected

LOC124902544 (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 (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902544	XR_007062369.1	n.3742+10112C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70571 AN: 151840 Hom.: 17215 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.465 AC: 70616 AN: 151960 Hom.: 17235 Cov.: 32 AF XY: 0.464 AC XY: 34466 AN XY: 74282

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.482

Alfa AF: 0.492 Hom.: 3182

Bravo AF: 0.451

Asia WGS AF: 0.619 AC: 2151 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	2.7
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928565; hg19: chr10-44832884;