rs493218

chr15-53198065-T-C

Variant summary

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

The XR_932257.3(LOC107983981):n.696+4222T>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 0.154 in 152,170 control chromosomes in the GnomAD database, including 2,211 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 0.15 (2211 hom., cov: 32)
• Consequence: LOC107983981 XR_932257.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107983981	XR_004837531.2	n.481-23361T>C		intron_variant, non_coding_transcript_variant
LOC107983981	XR_932257.3	n.696+4222T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23350 AN: 152050 Hom.: 2200 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.154 AC: 23379 AN: 152170 Hom.: 2211 Cov.: 32 AF XY: 0.155 AC XY: 11500 AN XY: 74390

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.0573

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.161

Alfa AF: 0.124 Hom.: 601

Bravo AF: 0.167

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	3.6
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs493218; hg19: chr15-53490262;