chr22-46111790-T-C

Position:

• chr22-46111790-T-C

Variant summary

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

The XM_047441694.1(LOC124905135):​c.*7201T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,924 control chromosomes in the GnomAD database, including 7,123 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 0.29 (7119 hom., cov: 32)
  • Exomes 𝑓: 0.41 (4 hom.)
• Consequence: LOC124905135 XM_047441694.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

Genes affected

LOC124905135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905135	XM_047441694.1	c.*7201T>C		3_prime_UTR_variant	2/2		XP_047297650.1
LOC124905135	XM_047441695.1	c.*7201T>C		3_prime_UTR_variant	2/2		XP_047297651.1
LOC124905135	XM_047441696.1	c.*7201T>C		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.2422T>C		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44315 AN: 151760 Hom.: 7106 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00271

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.266

GnomAD4 exome AF: 0.413 AC: 19 AN: 46 Hom.: 4 Cov.: 0 AF XY: 0.444 AC XY: 16 AN XY: 36

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.409

GnomAD4 genome AF: 0.292 AC: 44360 AN: 151878 Hom.: 7119 Cov.: 32 AF XY: 0.290 AC XY: 21565 AN XY: 74236

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.263

Alfa AF: 0.276 Hom.: 7172

Bravo AF: 0.291

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11090910; hg19: chr22-46507670;