rs62057608

Positions:

• chr16-35447822-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000562068.2(ZNF971P):​n.325G>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 0.0266 in 454,902 control chromosomes in the GnomAD database, including 242 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 0.026 (64 hom., cov: 34)
  • Exomes 𝑓: 0.027 (178 hom.)
• Consequence: ZNF971P ENST00000562068.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

Genes affected

ZNF971P (HGNC:51848): (zinc finger protein 971, pseudogene)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0259 (3939/152246) while in subpopulation NFE AF= 0.0401 (2724/68000). AF 95% confidence interval is 0.0388. There are 64 homozygotes in gnomad4. There are 1863 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 64 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF971P	ENST00000562068.2	n.325G>A		non_coding_transcript_exon_variant	1/1
	ENST00000568619.2			downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.0259 AC: 3939 AN: 152128 Hom.: 64 Cov.: 34

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0160

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0234

GnomAD3 exomes AF: 0.0216 AC: 2981 AN: 138018 Hom.: 54 AF XY: 0.0207 AC XY: 1542 AN XY: 74632

Gnomad AFR exome AF: 0.0106

Gnomad AMR exome AF: 0.0111

Gnomad ASJ exome AF: 0.0141

Gnomad EAS exome AF: 0.0000954

Gnomad SAS exome AF: 0.00295

Gnomad FIN exome AF: 0.0370

Gnomad NFE exome AF: 0.0383

Gnomad OTH exome AF: 0.0253

GnomAD4 exome AF: 0.0269 AC: 8141 AN: 302656 Hom.: 178 Cov.: 0 AF XY: 0.0248 AC XY: 4273 AN XY: 172262

Gnomad4 AFR exome AF: 0.0115

Gnomad4 AMR exome AF: 0.0114

Gnomad4 ASJ exome AF: 0.0136

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00304

Gnomad4 FIN exome AF: 0.0396

Gnomad4 NFE exome AF: 0.0412

Gnomad4 OTH exome AF: 0.0270

GnomAD4 genome AF: 0.0259 AC: 3939 AN: 152246 Hom.: 64 Cov.: 34 AF XY: 0.0250 AC XY: 1863 AN XY: 74442

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.0160

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00331

Gnomad4 FIN AF: 0.0363

Gnomad4 NFE AF: 0.0401

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0315 Hom.: 25

Bravo AF: 0.0238

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62057608; hg19: chr16-34682193;