rs6506336

chr18-5843070-T-C

Variant summary

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

The NR_172496.1(MIR3976HG):n.603-33183T>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 0.121 in 152,154 control chromosomes in the GnomAD database, including 1,979 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 0.12 (1979 hom., cov: 33)
• Consequence: MIR3976HG NR_172496.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

MIR3976HG (HGNC:51104): (MIR3976 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3976HG	NR_172496.1	n.603-33183T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3976HG	ENST00000562452.2	n.479-33183T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18376 AN: 152036 Hom.: 1974 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.121 AC: 18410 AN: 152154 Hom.: 1979 Cov.: 33 AF XY: 0.121 AC XY: 8966 AN XY: 74392

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.0645

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0490

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0649 Hom.: 987

Bravo AF: 0.133

Asia WGS AF: 0.114 AC: 398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.58
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6506336; hg19: chr18-5843069;