chr13-77447083-G-A

Position:

• chr13-77447083-G-A

Variant summary

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

The XR_007063828.1(LOC124903186):​n.94-5332G>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 0.238 in 152,174 control chromosomes in the GnomAD database, including 5,054 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 0.24 (5054 hom., cov: 32)
• Consequence: LOC124903186 XR_007063828.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

Genes affected

LOC124903186 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903186	XR_007063828.1	n.94-5332G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36125 AN: 152056 Hom.: 5043 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.238 AC: 36149 AN: 152174 Hom.: 5054 Cov.: 32 AF XY: 0.237 AC XY: 17660 AN XY: 74396

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.0703

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.225

Alfa AF: 0.289 Hom.: 13254

Bravo AF: 0.224

Asia WGS AF: 0.177 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7317940; hg19: chr13-78021218;