rs10499074

chr6-113557780-C-G

Variant summary

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

The XR_007059713.1(LOC124901379):n.246+29394G>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 0.0184 in 152,248 control chromosomes in the GnomAD database, including 78 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 0.018 (78 hom., cov: 32)
• Consequence: LOC124901379 XR_007059713.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

LOC124901379 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901379	XR_007059713.1	n.246+29394G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0183 AC: 2787 AN: 152130 Hom.: 78 Cov.: 32

Gnomad AFR AF: 0.00630

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0686

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.00757

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0184 AC: 2797 AN: 152248 Hom.: 78 Cov.: 32 AF XY: 0.0203 AC XY: 1515 AN XY: 74456

Gnomad4 AFR AF: 0.00635

Gnomad4 AMR AF: 0.0690

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0537

Gnomad4 FIN AF: 0.00160

Gnomad4 NFE AF: 0.00757

Gnomad4 OTH AF: 0.0340

Alfa AF: 0.00969 Hom.: 3

Bravo AF: 0.0230

Asia WGS AF: 0.0850 AC: 297 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.7
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499074; hg19: chr6-113878982;