rs4917589

Positions:

• chr10-110853044-A-G
• chr10-110853044-A-T

Variant summary

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

The XR_007062287.1(LOC124902499):​n.223-103T>C 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 0.777 in 152,018 control chromosomes in the GnomAD database, including 46,882 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 0.78 (46882 hom., cov: 30)
• Consequence: LOC124902499 XR_007062287.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

Genes affected

LOC124902499 (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 (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902499	XR_007062287.1	n.223-103T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118090 AN: 151900 Hom.: 46853 Cov.: 30

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.777 AC: 118160 AN: 152018 Hom.: 46882 Cov.: 30 AF XY: 0.781 AC XY: 58051 AN XY: 74316

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.776

Alfa AF: 0.830 Hom.: 70378

Bravo AF: 0.775

Asia WGS AF: 0.846 AC: 2940 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	1.2
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4917589; hg19: chr10-112612802;