chr13-76476277-G-A

Position:

• chr13-76476277-G-A

Variant summary

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

The XR_001749919.1(LOC105370263):​n.157+13414G>A 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 0.45 in 151,810 control chromosomes in the GnomAD database, including 15,618 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 0.45 (15618 hom., cov: 31)
• Consequence: LOC105370263 XR_001749919.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

LOC105370263 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370263	XR_001749919.1	n.157+13414G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68334 AN: 151690 Hom.: 15606 Cov.: 31

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.450 AC: 68388 AN: 151810 Hom.: 15618 Cov.: 31 AF XY: 0.450 AC XY: 33392 AN XY: 74174

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.425

Alfa AF: 0.470 Hom.: 8946

Bravo AF: 0.431

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.5
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs511512; hg19: chr13-77050413;