chr11-82540628-C-G

Variant names:

• chr11-82540628-C-G
• rs1939638
• ENST00000532217.1:n.440+132464G>C

Variant summary

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

The ENST00000532217.1(MIR4300HG):​n.440+132464G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.99 in 152,348 control chromosomes in the GnomAD database, including 74,732 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 0.99 (74732 hom., cov: 32)
• Consequence: MIR4300HG ENST00000532217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

MIR4300HG (HGNC:52003): (MIR4300 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4300HG	ENST00000532217.1	n.440+132464G>C		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.990 AC: 150774 AN: 152230 Hom.: 74674 Cov.: 32

Gnomad AFR AF: 0.997

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.991

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.994

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

GnomAD4 genome AF: 0.990 AC: 150891 AN: 152348 Hom.: 74732 Cov.: 32 AF XY: 0.991 AC XY: 73805 AN XY: 74494

Gnomad4 AFR AF: 0.997

Gnomad4 AMR AF: 0.981

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.997

Gnomad4 FIN AF: 0.991

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.994

Alfa AF: 0.988 Hom.: 8639

Bravo AF: 0.989

Asia WGS AF: 0.997 AC: 3468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.28
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1939638; hg19: chr11-82251670;