13-104808311-T-C

Variant summary

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

The XR_001749995.2(LOC107984606):n.296+28892A>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 0.924 in 152,198 control chromosomes in the GnomAD database, including 65,493 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 0.92 (65493 hom., cov: 32)
• Consequence: LOC107984606 XR_001749995.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

Genes affected

LOC107984606 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984606	XR_001749995.2	n.296+28892A>G		intron_variant, non_coding_transcript_variant
LOC107984606	XR_001749993.2	n.422-2693A>G		intron_variant, non_coding_transcript_variant
LOC107984606	XR_001749994.2	n.297-2693A>G		intron_variant, non_coding_transcript_variant
LOC107984606	XR_007063859.1	n.421+15352A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140541 AN: 152080 Hom.: 65461 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.924 AC: 140632 AN: 152198 Hom.: 65493 Cov.: 32 AF XY: 0.927 AC XY: 68953 AN XY: 74418

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.953

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.979

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.925

Alfa AF: 0.961 Hom.: 8926

Bravo AF: 0.915

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.4
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs323425; hg19: chr13-105460662;