rs13220542

chr6-90909043-A-G

Variant summary

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

The XR_001744259.1(LOC107986623):n.1349+882A>G 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 0.104 in 152,216 control chromosomes in the GnomAD database, including 894 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 0.10 (894 hom., cov: 32)
• Consequence: LOC107986623 XR_001744259.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

LOC107986623 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986623	XR_001744259.1	n.1349+882A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15847 AN: 152098 Hom.: 893 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0977

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.104 AC: 15849 AN: 152216 Hom.: 894 Cov.: 32 AF XY: 0.107 AC XY: 7993 AN XY: 74404

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0977

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0968 Hom.: 107

Bravo AF: 0.104

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.1
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13220542; hg19: chr6-91618761;