rs10494915

chr1-209068535-A-G

Variant summary

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

The XR_001738442.2(LOC107985255):n.495+64219T>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 0.16 in 152,204 control chromosomes in the GnomAD database, including 2,221 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 (2221 hom., cov: 33)
• Consequence: LOC107985255 XR_001738442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.63

Genes affected

LOC107985255 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985255	XR_001738442.2	n.495+64219T>C		intron_variant, non_coding_transcript_variant
LOC107985255	XR_001738441.2	n.495+64219T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24336 AN: 152086 Hom.: 2215 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.160 AC: 24361 AN: 152204 Hom.: 2221 Cov.: 33 AF XY: 0.156 AC XY: 11608 AN XY: 74440

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0927

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.154

Alfa AF: 0.139 Hom.: 814

Bravo AF: 0.165

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	15
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494915; hg19: chr1-209241880;