12-48335371-C-A

Position:

• chr12-48335371-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001365804.1(ZNF641):​c.*1701G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 152,234 control chromosomes in the GnomAD database, including 31 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 0.018 (31 hom., cov: 32)
• Consequence: ZNF641 NM_001365804.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858

Genes affected

ZNF641 (HGNC:31834): (zinc finger protein 641) Predicted to enable DNA-binding transcription factor 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. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0183 (2792/152234) while in subpopulation NFE AF= 0.028 (1907/68000). AF 95% confidence interval is 0.027. There are 31 homozygotes in gnomad4. There are 1357 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 31 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF641	NM_001365804.1	c.*1701G>T		3_prime_UTR_variant	6/6		NP_001352733.1
ZNF641	XM_005268640.6	c.*1701G>T		3_prime_UTR_variant	6/6		XP_005268697.1
		n.48335371C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2793 AN: 152118 Hom.: 31 Cov.: 32

Gnomad AFR AF: 0.00343

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0192

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

GnomAD4 genome AF: 0.0183 AC: 2792 AN: 152234 Hom.: 31 Cov.: 32 AF XY: 0.0182 AC XY: 1357 AN XY: 74440

Gnomad4 AFR AF: 0.00342

Gnomad4 AMR AF: 0.0118

Gnomad4 ASJ AF: 0.0340

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00498

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0280

Gnomad4 OTH AF: 0.0190

Alfa AF: 0.0252 Hom.: 72

Bravo AF: 0.0160

Asia WGS AF: 0.00231 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2450993; hg19: chr12-48729154;