rs10232364

chr7-112350947-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431064.1(ZNF277-AS1):n.352-22549C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,286 control chromosomes in the GnomAD database, including 346 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 0.044 (346 hom., cov: 32)
• Consequence: ZNF277-AS1 ENST00000431064.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800

Genes affected

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

LOC124901728 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901728	XR_007060480.1	n.157-9825C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF277-AS1	ENST00000431064.1	n.352-22549C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0437 AC: 6650 AN: 152168 Hom.: 344 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.00621

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0438 AC: 6674 AN: 152286 Hom.: 346 Cov.: 32 AF XY: 0.0420 AC XY: 3129 AN XY: 74454

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0223

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.00621

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0285 Hom.: 33

Bravo AF: 0.0484

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.9
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10232364; hg19: chr7-111991002;