rs7226835

Variant names:

• chr18-39585341-C-A
• rs7226835
• ENST00000591629.2:n.283-49726G>T

Variant summary

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

The ENST00000591629.2(MIR924HG):​n.283-49726G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0753 in 152,184 control chromosomes in the GnomAD database, including 496 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 0.075 (496 hom., cov: 32)
• Consequence: MIR924HG ENST00000591629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 5 publications found

Genes affected

MIR924HG (HGNC:44332): (MIR924 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0965 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000591629.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR924HG	NR_024391.1		n.124-49726G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR924HG	ENST00000591629.2	TSL:2	n.283-49726G>T		intron	N/A
	MIR924HG	ENST00000652839.1		n.270-49726G>T		intron	N/A
	MIR924HG	ENST00000652860.2		n.279-49726G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0754 AC: 11460 AN: 152066 Hom.: 496 Cov.: 32

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.00830

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.0542

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

GnomAD4 genome AF: 0.0753 AC: 11462 AN: 152184 Hom.: 496 Cov.: 32 AF XY: 0.0746 AC XY: 5547 AN XY: 74392

African (AFR) AF: 0.0507 AC: 2104 AN: 41532

American (AMR) AF: 0.0477 AC: 730 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0642 AC: 223 AN: 3472

East Asian (EAS) AF: 0.00832 AC: 43 AN: 5166

South Asian (SAS) AF: 0.0814 AC: 392 AN: 4816

European-Finnish (FIN) AF: 0.0989 AC: 1047 AN: 10584

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0985 AC: 6699 AN: 68006

Other (OTH) AF: 0.0537 AC: 113 AN: 2106

Alfa AF: 0.0765 Hom.: 320

Bravo AF: 0.0697

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.64
DANN	Benign	0.19
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7226835;

hg19: chr18-37165305;