rs10404342

Variant names:

• chr19-56620870-C-A
• rs10404342
• NM_001370215.1:c.161-398C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

ENSG00000293626 (HGNC:):

ZIM2-AS1 (HGNC:51304): (ZIM2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370215.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF71	NM_001370215.1	MANE Select	c.161-398C>A		intron	N/A	NP_001357144.1	M0R0C0
	ZNF71	NM_001370214.1		c.-20-398C>A		intron	N/A	NP_001357143.1	Q9NQZ8
	ZNF71	NM_021216.5		c.-20-398C>A		intron	N/A	NP_067039.1	Q9NQZ8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF71	ENST00000599599.7	TSL:2 MANE Select	c.161-398C>A		intron	N/A	ENSP00000471138.2	M0R0C0
	ZNF71	ENST00000328070.10	TSL:1	c.-20-398C>A		intron	N/A	ENSP00000328245.5	Q9NQZ8
	ENSG00000293626	ENST00000716550.1		n.160+6932C>A		intron	N/A	ENSP00000520562.1	A0ABB0MV33

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

African (AFR) AF: 0.285 AC: 11802 AN: 41468

American (AMR) AF: 0.201 AC: 3069 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0695 AC: 241 AN: 3470

East Asian (EAS) AF: 0.600 AC: 3083 AN: 5140

South Asian (SAS) AF: 0.348 AC: 1677 AN: 4824

European-Finnish (FIN) AF: 0.0766 AC: 811 AN: 10588

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5639 AN: 68016

Other (OTH) AF: 0.157 AC: 331 AN: 2112

Alfa AF: 0.125 Hom.: 3976

Bravo AF: 0.191

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.69
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10404342; hg19: chr19-57132238; COSMIC: COSV107397484;