rs4773094

Positions:

• chr13-109789136-G-A
• chr13-109789136-G-C

Variant summary

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

The XM_047430835.1(LOC124903211):​c.*1299G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,102 control chromosomes in the GnomAD database, including 4,469 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 (4469 hom., cov: 33)
• Consequence: LOC124903211 XM_047430835.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

Genes affected

LOC124903211 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903211	XM_047430835.1	c.*1299G>A		3_prime_UTR_variant	2/2		XP_047286791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000275741	ENST00000615635.1	n.115+3191G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36564 AN: 151984 Hom.: 4471 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.240 AC: 36573 AN: 152102 Hom.: 4469 Cov.: 33 AF XY: 0.240 AC XY: 17842 AN XY: 74346

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.269

Alfa AF: 0.249 Hom.: 7843

Bravo AF: 0.236

Asia WGS AF: 0.253 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4773094; hg19: chr13-110441483;