rs2249151

Variant names:

• chr7-112346748-C-A
• rs2249151
• ENST00000411413.1:n.78+3716G>T

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 ENST00000411413.1(ZNF277-AS1):​n.78+3716G>T variant causes a intron 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-AS1 ENST00000411413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 1 publications found

Genes affected

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF277-AS1	NR_186626.1	n.78+3716G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF277-AS1	ENST00000411413.1	n.78+3716G>T		intron_variant	Intron 1 of 2	5
ZNF277-AS1	ENST00000431064.1	n.352-18350G>T		intron_variant	Intron 3 of 3	3
ZNF277-AS1	ENST00000847105.1	n.283-18350G>T		intron_variant	Intron 2 of 2

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 v4.3

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;