rs308097

Positions:

• chr7-5840746-G-A
• chr7-5840746-G-C
• chr7-5840746-G-T

Variant summary

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

The ENST00000421890.5(ENSG00000291099):​n.696G>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 0.0464 in 456,478 control chromosomes in the GnomAD database, including 746 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 0.035 (137 hom., cov: 32)
  • Exomes 𝑓: 0.052 (609 hom.)
• Consequence: ENSG00000291099 ENST00000421890.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

Genes affected

ENSG00000291099 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF815P	NR_023382.1	n.593G>A		non_coding_transcript_exon_variant	4/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291099	ENST00000421890.5	n.696G>A		non_coding_transcript_exon_variant	5/6	2
ZNF815P	ENST00000434898.6	n.649G>A		non_coding_transcript_exon_variant	5/6	6
ENSG00000291099	ENST00000686456.1	n.625G>A		non_coding_transcript_exon_variant	4/5

Frequencies

GnomAD3 genomes AF: 0.0347 AC: 5273 AN: 152068 Hom.: 137 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.0322

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.0122

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.0379

GnomAD4 exome AF: 0.0524 AC: 15935 AN: 304292 Hom.: 609 Cov.: 0 AF XY: 0.0586 AC XY: 10152 AN XY: 173286

Gnomad4 AFR exome AF: 0.0142

Gnomad4 AMR exome AF: 0.0214

Gnomad4 ASJ exome AF: 0.0446

Gnomad4 EAS exome AF: 0.0248

Gnomad4 SAS exome AF: 0.103

Gnomad4 FIN exome AF: 0.0154

Gnomad4 NFE exome AF: 0.0461

Gnomad4 OTH exome AF: 0.0453

GnomAD4 genome AF: 0.0346 AC: 5268 AN: 152186 Hom.: 137 Cov.: 32 AF XY: 0.0338 AC XY: 2513 AN XY: 74402

Gnomad4 AFR AF: 0.0138

Gnomad4 AMR AF: 0.0279

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.0983

Gnomad4 FIN AF: 0.0122

Gnomad4 NFE AF: 0.0464

Gnomad4 OTH AF: 0.0375

Alfa AF: 0.0363 Hom.: 25

Bravo AF: 0.0336

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.099
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs308097; hg19: chr7-5880377;