17-6941095-G-A

Variant names:

• chr17-6941095-G-A
• rs1696
• ENST00000570562.5:n.238-60033C>T

Variant summary

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

The ENST00000570562.5(MIR497HG):​n.238-60033C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,006 control chromosomes in the GnomAD database, including 1,435 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 (1435 hom., cov: 31)
• Consequence: MIR497HG ENST00000570562.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• Publications: 4 publications found

Genes affected

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

ALOX12P2 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000570562.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR497HG	ENST00000570562.5	TSL:3	n.238-60033C>T		intron	N/A
	MIR497HG	ENST00000572385.6	TSL:4	n.234-60033C>T		intron	N/A
	ALOX12P2	ENST00000574183.1	TSL:3	n.73-12566G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17580 AN: 151888 Hom.: 1426 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.116 AC: 17613 AN: 152006 Hom.: 1435 Cov.: 31 AF XY: 0.112 AC XY: 8344 AN XY: 74304

African (AFR) AF: 0.230 AC: 9543 AN: 41428

American (AMR) AF: 0.0831 AC: 1269 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 432 AN: 3468

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5186

South Asian (SAS) AF: 0.0793 AC: 382 AN: 4818

European-Finnish (FIN) AF: 0.0560 AC: 591 AN: 10554

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0749 AC: 5088 AN: 67960

Other (OTH) AF: 0.109 AC: 230 AN: 2114

Alfa AF: 0.0878 Hom.: 573

Bravo AF: 0.122

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1696; hg19: chr17-6844414;