rs2450993

Variant names:

• chr12-48335371-C-A
• rs2450993
• NM_001365804.1:c.*1701G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-48335371-C-A
• chr12-48335371-C-G
• chr12-48335371-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

ENSG00000293682 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 31 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF641	NM_001365804.1	c.*1701G>T		3_prime_UTR_variant	Exon 6 of 6		NP_001352733.1
ZNF641	XM_005268640.6	c.*1701G>T		3_prime_UTR_variant	Exon 6 of 6		XP_005268697.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293682	ENST00000717861.1	n.312-22082C>A		intron_variant	Intron 3 of 4
ENSG00000257735	ENST00000717862.1	n.400+20049C>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.00342 AC: 142 AN: 41538

American (AMR) AF: 0.0118 AC: 181 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.00498 AC: 24 AN: 4818

European-Finnish (FIN) AF: 0.0309 AC: 328 AN: 10612

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0280 AC: 1907 AN: 68000

Other (OTH) AF: 0.0190 AC: 40 AN: 2110

Alfa AF: 0.0240 Hom.: 87

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
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs2450993; hg19: chr12-48729154;