6-33215953-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF70P1		n.33215953T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF70P1	ENST00000417480.1	n.249T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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;