rs10474433

chr5-75321018-T-Cchr5-75321018-T-G

Variant summary

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

The XR_007058824.1(LOC124901007):n.113A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,070 control chromosomes in the GnomAD database, including 10,087 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 0.36 (10087 hom., cov: 33)
• Consequence: LOC124901007 XR_007058824.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616

Genes affected

LOC124901007 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901007	XR_007058824.1	n.113A>G		non_coding_transcript_exon_variant	1/2
LOC124901007	XR_007058825.1	n.113A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000501886.2	n.199-535A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55104 AN: 151952 Hom.: 10078 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.363 AC: 55145 AN: 152070 Hom.: 10087 Cov.: 33 AF XY: 0.366 AC XY: 27234 AN XY: 74352

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.367

Alfa AF: 0.357 Hom.: 20186

Bravo AF: 0.356

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.3
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10474433; hg19: chr5-74616843;