rs274546

Positions:

• chr5-132364175-A-G
• chr5-132364175-A-T

Variant summary

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

The NR_110997.1(MIR3936HG):​n.380+760T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,004 control chromosomes in the GnomAD database, including 30,444 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 0.62 (30444 hom., cov: 32)
• Consequence: MIR3936HG NR_110997.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3936HG	NR_110997.1	n.380+760T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3936HG	ENST00000621103.4	n.380+760T>C		intron_variant, non_coding_transcript_variant		1
MIR3936HG	ENST00000649993.1	n.741+760T>C		intron_variant, non_coding_transcript_variant
MIR3936HG	ENST00000669845.1	n.186+2393T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94889 AN: 151884 Hom.: 30413 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.625 AC: 94975 AN: 152004 Hom.: 30444 Cov.: 32 AF XY: 0.614 AC XY: 45597 AN XY: 74280

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.629

Alfa AF: 0.614 Hom.: 51271

Bravo AF: 0.649

Asia WGS AF: 0.396 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.8
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs274546; hg19: chr5-131699867;