rs9960

Variant names:

• chr1-42852122-G-A
• rs9960
• NM_001242739.2:c.*309G>A

Variant summary

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

The NM_001242739.2(ZNF691):​c.*309G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 473,662 control chromosomes in the GnomAD database, including 6,869 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 0.17 (2310 hom., cov: 32)
  • Exomes 𝑓: 0.16 (4559 hom.)
• Consequence: ZNF691 NM_001242739.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 28 publications found

Genes affected

ZNF691 (HGNC:28028): (zinc finger protein 691) Predicted to enable DNA-binding transcription factor activity 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 located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF691-DT (HGNC:55800): (ZNF691 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001242739.2. 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
	ZNF691	NM_001242739.2	MANE Select	c.*309G>A		3_prime_UTR	Exon 4 of 4	NP_001229668.1	Q5VV52-2
	ZNF691	NM_015911.4		c.*309G>A		3_prime_UTR	Exon 2 of 2	NP_056995.1	Q5VV52-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF691	ENST00000651192.1	MANE Select	c.*309G>A		3_prime_UTR	Exon 4 of 4	ENSP00000498913.1	Q5VV52-2
	ZNF691	ENST00000372508.7	TSL:1	c.*309G>A		3_prime_UTR	Exon 2 of 2	ENSP00000361586.3	Q5VV52-3
	ZNF691	ENST00000372502.5	TSL:2	c.*309G>A		3_prime_UTR	Exon 4 of 4	ENSP00000361580.2	Q5VV52-2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25721 AN: 152076 Hom.: 2306 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.167

GnomAD4 exome AF: 0.162 AC: 52130 AN: 321468 Hom.: 4559 Cov.: 2 AF XY: 0.162 AC XY: 28114 AN XY: 173846

African (AFR) AF: 0.178 AC: 1594 AN: 8956

American (AMR) AF: 0.223 AC: 3338 AN: 14936

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 1193 AN: 8770

East Asian (EAS) AF: 0.000603 AC: 10 AN: 16570

South Asian (SAS) AF: 0.157 AC: 7048 AN: 44874

European-Finnish (FIN) AF: 0.144 AC: 4126 AN: 28580

Middle Eastern (MID) AF: 0.129 AC: 160 AN: 1244

European-Non Finnish (NFE) AF: 0.176 AC: 31839 AN: 180680

Other (OTH) AF: 0.167 AC: 2822 AN: 16858

GnomAD4 genome AF: 0.169 AC: 25740 AN: 152194 Hom.: 2310 Cov.: 32 AF XY: 0.166 AC XY: 12375 AN XY: 74410

African (AFR) AF: 0.178 AC: 7407 AN: 41530

American (AMR) AF: 0.198 AC: 3026 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5188

South Asian (SAS) AF: 0.158 AC: 760 AN: 4820

European-Finnish (FIN) AF: 0.138 AC: 1459 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12085 AN: 67986

Other (OTH) AF: 0.165 AC: 349 AN: 2112

Alfa AF: 0.174 Hom.: 7863

Bravo AF: 0.174

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.2
DANN	Benign	0.74
PhyloP100		0.14
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: rs9960; hg19: chr1-43317793; COSMIC: COSV65289896; COSMIC: COSV65289896;