rs3744749

Positions:

• chr22-46058328-G-A
• chr22-46058328-G-C

Variant summary

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

The XM_047441696.1(LOC124905135):​c.-5555+13321G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,124 control chromosomes in the GnomAD database, including 4,121 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 0.20 (4121 hom., cov: 33)
• Consequence: LOC124905135 XM_047441696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

LOC124905135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905135	XM_047441696.1	c.-5555+13321G>A		intron_variant			XP_047297652.1
PRR34-AS1	NR_027034.1	n.1441G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIRLET7BHG	ENST00000381051.6	n.52+4408G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29826 AN: 152004 Hom.: 4098 Cov.: 33

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.197 AC: 29906 AN: 152124 Hom.: 4121 Cov.: 33 AF XY: 0.192 AC XY: 14279 AN XY: 74386

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0759

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.195

Alfa AF: 0.133 Hom.: 2178

Bravo AF: 0.211

Asia WGS AF: 0.130 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3744749; hg19: chr22-46454208;