rs2249151

Variant names:

• chr7-112346748-C-A
• rs2249151
• ENST00000421864.3:c.*4019C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-112346748-C-A
• chr7-112346748-C-T

Variant summary

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

The ENST00000421864.3(ZNF277):​c.*4019C>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 0.346 in 151,994 control chromosomes in the GnomAD database, including 11,511 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 0.35 (11511 hom., cov: 32)
• Consequence: ZNF277 ENST00000421864.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 1 publications found

Genes affected

ZNF277 (HGNC:13070): (zinc finger protein 277) Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and metal ion binding activity. Predicted to act upstream of or within cellular response to hydrogen peroxide and regulation of cellular senescence. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF277-AS1 (HGNC:55828): (ZNF277 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421864.3. 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
	ZNF277-AS1	NR_186626.1		n.78+3716G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF277	ENST00000421864.3	TSL:3	c.*4019C>A		3_prime_UTR	Exon 12 of 12	ENSP00000415735.3
	ZNF277-AS1	ENST00000411413.1	TSL:5	n.78+3716G>T		intron	N/A
	ZNF277-AS1	ENST00000431064.1	TSL:3	n.352-18350G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52445 AN: 151876 Hom.: 11471 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.346 AC: 52547 AN: 151994 Hom.: 11511 Cov.: 32 AF XY: 0.342 AC XY: 25397 AN XY: 74296

African (AFR) AF: 0.621 AC: 25708 AN: 41408

American (AMR) AF: 0.318 AC: 4868 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1177 AN: 3466

East Asian (EAS) AF: 0.172 AC: 889 AN: 5176

South Asian (SAS) AF: 0.346 AC: 1668 AN: 4826

European-Finnish (FIN) AF: 0.177 AC: 1871 AN: 10556

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 15263 AN: 67958

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.262 Hom.: 7472

Bravo AF: 0.368

Asia WGS AF: 0.297 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.28
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2249151; hg19: chr7-111986803;