chr22-46113090-G-A

Variant names:

• chr22-46113090-G-A
• rs9627620
• ENST00000360737.4:n.3722G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000360737.4(MIRLET7BHG):​n.3722G>A 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 0.0016 in 268,916 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0027 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00015 (0 hom.)
• Consequence: MIRLET7BHG ENST00000360737.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 1 publications found

Genes affected

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

LOC124905135 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIRLET7BHG	NR_027033.2	n.3879G>A		non_coding_transcript_exon_variant	Exon 6 of 6
MIRLET7BHG	NR_110479.1	n.3728G>A		non_coding_transcript_exon_variant	Exon 5 of 5
LOC124905135	XM_047441694.1	c.*8501G>A		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.3722G>A		non_coding_transcript_exon_variant	Exon 5 of 5	2
MIRLET7BHG	ENST00000794300.1	n.950G>A		non_coding_transcript_exon_variant	Exon 6 of 6
MIRLET7BHG	ENST00000794301.1	n.831G>A		non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.00270 AC: 411 AN: 152140 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00951

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00287

GnomAD4 exome AF: 0.000154 AC: 18 AN: 116658 Hom.: 0 Cov.: 0 AF XY: 0.0000945 AC XY: 6 AN XY: 63514

African (AFR) AF: 0.00670 AC: 15 AN: 2240

American (AMR) AF: 0.000203 AC: 1 AN: 4920

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2644

East Asian (EAS) AF: 0.00 AC: 0 AN: 2974

South Asian (SAS) AF: 0.00 AC: 0 AN: 23832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5780

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 438

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68052

Other (OTH) AF: 0.000173 AC: 1 AN: 5778

GnomAD4 genome AF: 0.00270 AC: 411 AN: 152258 Hom.: 0 Cov.: 33 AF XY: 0.00259 AC XY: 193 AN XY: 74444

African (AFR) AF: 0.00948 AC: 394 AN: 41558

American (AMR) AF: 0.000588 AC: 9 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 68006

Other (OTH) AF: 0.00284 AC: 6 AN: 2110

Alfa AF: 0.00148 Hom.: 0

Bravo AF: 0.00291

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9627620; hg19: chr22-46508970;