rs3840880

Variant names:

• chr17-6994524-TC-T
• rs3840880
• ENST00000399541.7:n.250-8985delG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000399541.7(MIR497HG):​n.250-8985delG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,982 control chromosomes in the GnomAD database, including 24,355 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.56 (24355 hom., cov: 0)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: MIR497HG ENST00000399541.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 4 publications found

Genes affected

MIR497HG (HGNC:39523): (mir-497-195 cluster host gene)

ALOX12-AS1 (HGNC:51342): (ALOX12 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX12-AS1	NR_040089.1	n.234-8985delG		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR497HG	ENST00000399541.7	n.250-8985delG		intron_variant	Intron 2 of 2	2
MIR497HG	ENST00000570562.5	n.237+15271delG		intron_variant	Intron 2 of 3	3
MIR497HG	ENST00000572385.6	n.233+15271delG		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85301 AN: 151858 Hom.: 24331 Cov.: 0

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.562 AC: 85374 AN: 151976 Hom.: 24355 Cov.: 0 AF XY: 0.566 AC XY: 42042 AN XY: 74288

African (AFR) AF: 0.471 AC: 19523 AN: 41472

American (AMR) AF: 0.650 AC: 9916 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1864 AN: 3462

East Asian (EAS) AF: 0.587 AC: 3028 AN: 5162

South Asian (SAS) AF: 0.534 AC: 2573 AN: 4818

European-Finnish (FIN) AF: 0.649 AC: 6837 AN: 10534

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.585 AC: 39727 AN: 67950

Other (OTH) AF: 0.563 AC: 1187 AN: 2110

Alfa AF: 0.365 Hom.: 1218

Bravo AF: 0.557

Asia WGS AF: 0.550 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3840880; hg19: chr17-6897843;