rs12971799

Variant names:

• chr19-53163873-T-C
• rs12971799
• NM_024733.5:c.*580A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-53163873-T-C
• chr19-53163873-T-G

Variant summary

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

The NM_024733.5(ZNF665):​c.*580A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,084 control chromosomes in the GnomAD database, including 22,966 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 0.52 (22963 hom., cov: 32)
  • Exomes 𝑓: 0.42 (3 hom.)
• Consequence: ZNF665 NM_024733.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 3 publications found

Genes affected

ZNF665 (HGNC:25885): (zinc finger protein 665) 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. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF665	NM_024733.5	c.*580A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000396424.5	NP_079009.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF665	ENST00000396424.5	c.*580A>G		3_prime_UTR_variant	Exon 4 of 4	2	NM_024733.5	ENSP00000379702.2
ZNF665	ENST00000596564.1	n.27A>G		non_coding_transcript_exon_variant	Exon 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78455 AN: 151912 Hom.: 22950 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.519

GnomAD4 exome AF: 0.423 AC: 22 AN: 52 Hom.: 3 Cov.: 0 AF XY: 0.441 AC XY: 15 AN XY: 34

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.409 AC: 18 AN: 44

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.516 AC: 78498 AN: 152032 Hom.: 22963 Cov.: 32 AF XY: 0.524 AC XY: 38941 AN XY: 74308

African (AFR) AF: 0.230 AC: 9529 AN: 41504

American (AMR) AF: 0.616 AC: 9390 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3378 AN: 5144

South Asian (SAS) AF: 0.715 AC: 3452 AN: 4830

European-Finnish (FIN) AF: 0.667 AC: 7043 AN: 10564

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42142 AN: 67968

Other (OTH) AF: 0.520 AC: 1095 AN: 2104

Alfa AF: 0.550 Hom.: 18315

Bravo AF: 0.497

Asia WGS AF: 0.653 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.57
PhyloP100		-1.7

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: rs12971799; hg19: chr19-53667126;