chr6-33215953-T-C

Variant names:

• chr6-33215953-T-C
• rs213213
• ENST00000417480.1:n.249T>C

Variant summary

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

The ENST00000417480.1(ZNF70P1):​n.249T>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 0.748 in 152,700 control chromosomes in the GnomAD database, including 43,136 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 0.75 (43008 hom., cov: 33)
  • Exomes 𝑓: 0.70 (128 hom.)
• Consequence: ZNF70P1 ENST00000417480.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03
• Publications: 24 publications found

Genes affected

ZNF70P1 (HGNC:13846): (zinc finger protein 70 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417480.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF70P1	ENST00000417480.1	TSL:6	n.249T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113702 AN: 152098 Hom.: 42959 Cov.: 33

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.750

GnomAD4 exome AF: 0.705 AC: 341 AN: 484 Hom.: 128 Cov.: 0 AF XY: 0.722 AC XY: 260 AN XY: 360

African (AFR) AF: 0.800 AC: 8 AN: 10

American (AMR) AF: 0.750 AC: 6 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 5 AN: 6

East Asian (EAS) AF: 0.778 AC: 14 AN: 18

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.792 AC: 19 AN: 24

Middle Eastern (MID) AF: 0.833 AC: 5 AN: 6

European-Non Finnish (NFE) AF: 0.682 AC: 259 AN: 380

Other (OTH) AF: 0.767 AC: 23 AN: 30

GnomAD4 genome AF: 0.748 AC: 113809 AN: 152216 Hom.: 43008 Cov.: 33 AF XY: 0.750 AC XY: 55833 AN XY: 74404

African (AFR) AF: 0.824 AC: 34235 AN: 41550

American (AMR) AF: 0.767 AC: 11736 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2457 AN: 3470

East Asian (EAS) AF: 0.925 AC: 4784 AN: 5172

South Asian (SAS) AF: 0.841 AC: 4064 AN: 4830

European-Finnish (FIN) AF: 0.690 AC: 7316 AN: 10596

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46855 AN: 67984

Other (OTH) AF: 0.753 AC: 1590 AN: 2112

Alfa AF: 0.710 Hom.: 151902

Bravo AF: 0.759

Asia WGS AF: 0.824 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.27
DANN	Benign	0.51
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs213213; hg19: chr6-33183730;