rs272867

Variant names:

• chr5-132345364-G-A
• rs272867
• ENST00000621103.4:n.560+4451C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-132345364-G-A
• chr5-132345364-G-C
• chr5-132345364-G-T

Variant summary

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

The ENST00000621103.4(MIR3936HG):​n.560+4451C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,048 control chromosomes in the GnomAD database, including 27,742 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 0.60 (27742 hom., cov: 32)
• Consequence: MIR3936HG ENST00000621103.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 27 publications found

Genes affected

MIR3936HG (HGNC:40538): (MIR3936 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3936HG	NR_110997.1	n.560+4451C>T		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3936HG	ENST00000621103.4	n.560+4451C>T		intron_variant	Intron 5 of 7	1
MIR3936HG	ENST00000616965.1	n.343+4451C>T		intron_variant	Intron 3 of 4	5
MIR3936HG	ENST00000669845.1	n.187-10438C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90793 AN: 151928 Hom.: 27713 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.598 AC: 90876 AN: 152048 Hom.: 27742 Cov.: 32 AF XY: 0.587 AC XY: 43617 AN XY: 74322

African (AFR) AF: 0.655 AC: 27169 AN: 41472

American (AMR) AF: 0.650 AC: 9924 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3472

East Asian (EAS) AF: 0.331 AC: 1710 AN: 5164

South Asian (SAS) AF: 0.359 AC: 1731 AN: 4822

European-Finnish (FIN) AF: 0.488 AC: 5149 AN: 10552

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41022 AN: 67970

Other (OTH) AF: 0.612 AC: 1292 AN: 2112

Alfa AF: 0.607 Hom.: 87784

Bravo AF: 0.619

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs272867; hg19: chr5-131681057;