rs10404342

chr19-56620870-C-A

Variant summary

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

The NM_001370215.1(ZNF71):c.161-398C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,120 control chromosomes in the GnomAD database, including 3,583 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 0.18 (3583 hom., cov: 32)
• Consequence: ZNF71 NM_001370215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663

Genes affected

ZNF71 (HGNC:13141): (zinc finger protein 71) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF71-SMIM17 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF71	NM_001370215.1	c.161-398C>A		intron_variant		ENST00000599599.7
ZNF71-SMIM17	NR_163262.1	n.339+6932C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF71	ENST00000599599.7	c.161-398C>A		intron_variant		2	NM_001370215.1	P1
ZNF71	ENST00000328070.10	c.-20-398C>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26701 AN: 152002 Hom.: 3572 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.0766

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0829

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.176 AC: 26749 AN: 152120 Hom.: 3583 Cov.: 32 AF XY: 0.182 AC XY: 13533 AN XY: 74378

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.0766

Gnomad4 NFE AF: 0.0829

Gnomad4 OTH AF: 0.157

Alfa AF: 0.123 Hom.: 1138

Bravo AF: 0.191

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.3
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10404342; hg19: chr19-57132238;