chr18-5843070-T-C

Variant names:

• chr18-5843070-T-C
• rs6506336
• ENST00000654509.1:n.847T>C

Variant summary

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

The ENST00000654509.1(MIR3976HG):​n.847T>C variant causes a non coding transcript exon 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 ENST00000654509.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIR3976HG	NR_172494.1	n.603-35373T>C		intron_variant	Intron 4 of 8
MIR3976HG	NR_172495.1	n.603-33183T>C		intron_variant	Intron 4 of 9
MIR3976HG	NR_172496.1	n.603-33183T>C		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3976HG	ENST00000654509.1	n.847T>C		non_coding_transcript_exon_variant	Exon 4 of 4
MIR3976HG	ENST00000654839.1	n.972T>C		non_coding_transcript_exon_variant	Exon 5 of 5
MIR3976HG	ENST00000655587.1	n.1019T>C		non_coding_transcript_exon_variant	Exon 6 of 6

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

African (AFR) AF: 0.286 AC: 11857 AN: 41466

American (AMR) AF: 0.0645 AC: 985 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3470

East Asian (EAS) AF: 0.170 AC: 881 AN: 5174

South Asian (SAS) AF: 0.0958 AC: 462 AN: 4824

European-Finnish (FIN) AF: 0.0263 AC: 279 AN: 10616

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0490 AC: 3334 AN: 68008

Other (OTH) AF: 0.109 AC: 231 AN: 2116

Alfa AF: 0.0744 Hom.: 3103

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6506336; hg19: chr18-5843069;