rs308097

Variant names:

• chr7-5840746-G-A
• rs308097
• ENST00000421890.6:n.696G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000421890.6(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 ENST00000421890.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70
• Publications: 8 publications found

Genes affected

ENSG00000291099 (HGNC:):

ZNF815P (HGNC:22029): (zinc finger protein 815, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421890.6. 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
	ZNF815P	NR_023382.1		n.593G>A		non_coding_transcript_exon	Exon 4 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291099	ENST00000421890.6	TSL:2	n.696G>A		non_coding_transcript_exon	Exon 5 of 7
	ENSG00000291099	ENST00000430530.6	TSL:4	n.802G>A		non_coding_transcript_exon	Exon 6 of 7
	ZNF815P	ENST00000434898.6	TSL:6	n.649G>A		non_coding_transcript_exon	Exon 5 of 6

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

African (AFR) AF: 0.0142 AC: 122 AN: 8618

American (AMR) AF: 0.0214 AC: 583 AN: 27278

Ashkenazi Jewish (ASJ) AF: 0.0446 AC: 481 AN: 10784

East Asian (EAS) AF: 0.0248 AC: 228 AN: 9210

South Asian (SAS) AF: 0.103 AC: 6158 AN: 59730

European-Finnish (FIN) AF: 0.0154 AC: 197 AN: 12808

Middle Eastern (MID) AF: 0.0695 AC: 193 AN: 2776

European-Non Finnish (NFE) AF: 0.0461 AC: 7328 AN: 158862

Other (OTH) AF: 0.0453 AC: 645 AN: 14226

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

African (AFR) AF: 0.0138 AC: 575 AN: 41524

American (AMR) AF: 0.0279 AC: 426 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3470

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5172

South Asian (SAS) AF: 0.0983 AC: 473 AN: 4810

European-Finnish (FIN) AF: 0.0122 AC: 130 AN: 10620

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0464 AC: 3153 AN: 68014

Other (OTH) AF: 0.0375 AC: 79 AN: 2108

Alfa AF: 0.0368 Hom.: 25

Bravo AF: 0.0336

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.099
DANN	Benign	0.26
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs308097; hg19: chr7-5880377; COSMIC: COSV107517730;