rs4773094

Variant names:

• chr13-109789136-G-A
• rs4773094
• XM_047430835.1:c.*1299G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

LOC124903211 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124903211	XM_047430835.1	c.*1299G>A		3_prime_UTR_variant	Exon 2 of 2		XP_047286791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275741	ENST00000615635.1	n.115+3191G>A		intron_variant	Intron 1 of 2	4
ENSG00000275741	ENST00000772402.1	n.67+3191G>A		intron_variant	Intron 1 of 1
ENSG00000300543	ENST00000772621.1	n.157-6C>T		splice_region_variant, intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.231 AC: 9568 AN: 41486

American (AMR) AF: 0.207 AC: 3163 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 858 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1168 AN: 5178

South Asian (SAS) AF: 0.287 AC: 1386 AN: 4828

European-Finnish (FIN) AF: 0.257 AC: 2714 AN: 10574

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16743 AN: 67978

Other (OTH) AF: 0.269 AC: 567 AN: 2106

Alfa AF: 0.244 Hom.: 18649

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs4773094; hg19: chr13-110441483;