rs9904779

Variant names:

• chr17-6995296-C-G
• rs9904779
• ENST00000399541.7:n.250-9756G>C

Your query was ambiguous. Multiple possible variants found:

• chr17-6995296-C-G
• chr17-6995296-C-T

Variant summary

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

The ENST00000399541.7(MIR497HG):​n.250-9756G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,072 control chromosomes in the GnomAD database, including 24,304 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 0.56 (24282 hom., cov: 32)
  • Exomes 𝑓: 0.67 (22 hom.)
• Consequence: MIR497HG ENST00000399541.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448
• Publications: 15 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALOX12-AS1	NR_040089.1	n.234-9756G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR497HG	ENST00000399541.7	n.250-9756G>C		intron_variant	Intron 2 of 2	2
MIR497HG	ENST00000570562.5	n.237+14500G>C		intron_variant	Intron 2 of 3	3
MIR497HG	ENST00000572385.6	n.233+14500G>C		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84763 AN: 151862 Hom.: 24264 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.562

GnomAD4 exome AF: 0.674 AC: 62 AN: 92 Hom.: 22 AF XY: 0.720 AC XY: 36 AN XY: 50

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.600 AC: 6 AN: 10

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.800 AC: 8 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 40 AN: 60

Other (OTH) AF: 0.667 AC: 4 AN: 6

GnomAD4 genome AF: 0.558 AC: 84818 AN: 151980 Hom.: 24282 Cov.: 32 AF XY: 0.562 AC XY: 41728 AN XY: 74282

African (AFR) AF: 0.423 AC: 17517 AN: 41430

American (AMR) AF: 0.659 AC: 10071 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1997 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2687 AN: 5158

South Asian (SAS) AF: 0.541 AC: 2605 AN: 4814

European-Finnish (FIN) AF: 0.655 AC: 6929 AN: 10576

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41097 AN: 67940

Other (OTH) AF: 0.562 AC: 1185 AN: 2108

Alfa AF: 0.484 Hom.: 1513

Bravo AF: 0.552

Asia WGS AF: 0.536 AC: 1866 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.46
PhyloP100		0.45
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: rs9904779; hg19: chr17-6898615; COSMIC: COSV52349082;