13-59548619-G-A

Position:

• chr13-59548619-G-A

Variant summary

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

The XR_001749886.2(LOC107984625):​n.234-17231C>T 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 0.0462 in 152,118 control chromosomes in the GnomAD database, including 416 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 0.046 (416 hom., cov: 32)
• Consequence: LOC107984625 XR_001749886.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

Genes affected

LOC107984625 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984625	XR_001749886.2	n.234-17231C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0462 AC: 7019 AN: 152000 Hom.: 414 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0434

Gnomad ASJ AF: 0.00979

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00897

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0462 AC: 7023 AN: 152118 Hom.: 416 Cov.: 32 AF XY: 0.0487 AC XY: 3620 AN XY: 74340

Gnomad4 AFR AF: 0.0875

Gnomad4 AMR AF: 0.0433

Gnomad4 ASJ AF: 0.00979

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.00897

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.00372 Hom.: 3

Bravo AF: 0.0502

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs751531; hg19: chr13-60122753;