chr22-46111790-T-C

Variant names:

• chr22-46111790-T-C
• rs11090910
• ENST00000360737.4:n.2422T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000360737.4(MIRLET7BHG):​n.2422T>C variant causes a non coding transcript exon 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: MIRLET7BHG ENST00000360737.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 12 publications found

Genes affected

MIRLET7BHG (HGNC:37189): (MIRLET7B host gene)

LOC124905135 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIRLET7BHG	NR_027033.2	n.2579T>C		non_coding_transcript_exon_variant	Exon 6 of 6
MIRLET7BHG	NR_110479.1	n.2428T>C		non_coding_transcript_exon_variant	Exon 5 of 5
LOC124905135	XM_047441694.1	c.*7201T>C		3_prime_UTR_variant	Exon 2 of 2		XP_047297650.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIRLET7BHG	ENST00000360737.4	n.2422T>C		non_coding_transcript_exon_variant	Exon 5 of 5	2
MIRLET7BHG	ENST00000794298.1	n.455+1882T>C		intron_variant	Intron 5 of 5
MIRLET7BHG	ENST00000794300.1	n.554-904T>C		intron_variant	Intron 5 of 5

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.409 AC: 18 AN: 44

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.395 AC: 16347 AN: 41394

American (AMR) AF: 0.214 AC: 3270 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3468

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5158

South Asian (SAS) AF: 0.268 AC: 1290 AN: 4808

European-Finnish (FIN) AF: 0.287 AC: 3033 AN: 10554

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18724 AN: 67920

Other (OTH) AF: 0.263 AC: 554 AN: 2106

Alfa AF: 0.278 Hom.: 8574

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
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11090910; hg19: chr22-46507670;