rs17882539

Positions:

• chr7-95397096-G-A

Variant summary

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

The ENST00000702974.1(ENSG00000290101):​n.600G>A 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 0.291 in 152,012 control chromosomes in the GnomAD database, including 6,872 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 0.29 (6872 hom., cov: 32)
• Consequence: ENSG00000290101 ENST00000702974.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

Genes affected

ENSG00000290101 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986822	XR_001745283.2	n.557+68G>A		intron_variant
LOC107986822	XR_007060439.1	n.557+68G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290101	ENST00000702974.1	n.600G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44186 AN: 151894 Hom.: 6857 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.291 AC: 44225 AN: 152012 Hom.: 6872 Cov.: 32 AF XY: 0.300 AC XY: 22273 AN XY: 74322

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.259

Alfa AF: 0.258 Hom.: 5861

Bravo AF: 0.269

Asia WGS AF: 0.309 AC: 1075 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17882539; hg19: chr7-95026408; COSMIC: COSV55698242;