7-16850188-C-G

Position:

• chr7-16850188-C-G

Variant summary

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

The ENST00000603589.1(ENSG00000270593):​n.538G>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 0.574 in 159,868 control chromosomes in the GnomAD database, including 26,831 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 0.58 (25836 hom., cov: 32)
  • Exomes 𝑓: 0.49 (995 hom.)
• Consequence: ENSG00000270593 ENST00000603589.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

Genes affected

ENSG00000270593 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100287613		n.16850188C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000270593	ENST00000603589.1	n.538G>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87808 AN: 151948 Hom.: 25835 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.565

GnomAD4 exome AF: 0.492 AC: 3837 AN: 7802 Hom.: 995 Cov.: 0 AF XY: 0.502 AC XY: 2107 AN XY: 4198

Gnomad4 AFR exome AF: 0.545

Gnomad4 AMR exome AF: 0.396

Gnomad4 ASJ exome AF: 0.388

Gnomad4 EAS exome AF: 0.669

Gnomad4 SAS exome AF: 0.610

Gnomad4 FIN exome AF: 0.622

Gnomad4 NFE exome AF: 0.429

Gnomad4 OTH exome AF: 0.490

GnomAD4 genome AF: 0.578 AC: 87856 AN: 152066 Hom.: 25836 Cov.: 32 AF XY: 0.584 AC XY: 43389 AN XY: 74316

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.569

Alfa AF: 0.402 Hom.: 1013

Bravo AF: 0.573

Asia WGS AF: 0.755 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1525739; hg19: chr7-16889812;