rs738559

Positions:

• chr22-46113232-G-A

Variant summary

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

The XM_047441694.1(LOC124905135):​c.*8643G>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 0.0367 in 179,072 control chromosomes in the GnomAD database, including 180 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 0.037 (138 hom., cov: 33)
  • Exomes 𝑓: 0.038 (42 hom.)
• Consequence: LOC124905135 XM_047441694.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906

Genes affected

LOC124905135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905135	XM_047441694.1	c.*8643G>A		3_prime_UTR_variant	2/2		XP_047297650.1
LOC124905135	XM_047441695.1	c.*8643G>A		3_prime_UTR_variant	2/2		XP_047297651.1
LOC124905135	XM_047441696.1	c.*8643G>A		3_prime_UTR_variant	2/2		XP_047297652.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIRLET7BHG	ENST00000360737.4	n.3864G>A		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5572 AN: 152218 Hom.: 138 Cov.: 33

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0198

Gnomad FIN AF: 0.0395

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0517

Gnomad OTH AF: 0.0321

GnomAD4 exome AF: 0.0379 AC: 1012 AN: 26736 Hom.: 42 Cov.: 0 AF XY: 0.0352 AC XY: 500 AN XY: 14208

Gnomad4 AFR exome AF: 0.00701

Gnomad4 AMR exome AF: 0.0720

Gnomad4 ASJ exome AF: 0.0125

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0169

Gnomad4 FIN exome AF: 0.0326

Gnomad4 NFE exome AF: 0.0434

Gnomad4 OTH exome AF: 0.0246

GnomAD4 genome AF: 0.0366 AC: 5568 AN: 152336 Hom.: 138 Cov.: 33 AF XY: 0.0354 AC XY: 2641 AN XY: 74500

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.0588

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0395

Gnomad4 NFE AF: 0.0517

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0490 Hom.: 37

Bravo AF: 0.0382

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs738559; hg19: chr22-46509112;