chr16-72748925-A-G

Variant names:

• chr16-72748925-A-G
• rs292932
• ENST00000563328.5:n.326+1743A>G

Variant summary

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

The ENST00000563328.5(ZFHX3-AS1):​n.326+1743A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0331 in 152,310 control chromosomes in the GnomAD database, including 613 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 0.033 (613 hom., cov: 32)
• Consequence: ZFHX3-AS1 ENST00000563328.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 6 publications found

Genes affected

ZFHX3-AS1 (HGNC:56033): (ZFHX3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563328.5. 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
	ZFHX3-AS1	NR_171702.1		n.390+3459A>G		intron	N/A
	ZFHX3-AS1	NR_171703.1		n.347+3459A>G		intron	N/A
	ZFHX3-AS1	NR_171704.1		n.347+3459A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFHX3-AS1	ENST00000563328.5	TSL:3	n.326+1743A>G		intron	N/A
	ZFHX3-AS1	ENST00000653037.2		n.352+3459A>G		intron	N/A
	ZFHX3-AS1	ENST00000668995.1		n.400+3459A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0330 AC: 5026 AN: 152192 Hom.: 608 Cov.: 32

Gnomad AFR AF: 0.00569

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00188

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0331 AC: 5035 AN: 152310 Hom.: 613 Cov.: 32 AF XY: 0.0371 AC XY: 2767 AN XY: 74484

African (AFR) AF: 0.00568 AC: 236 AN: 41576

American (AMR) AF: 0.183 AC: 2795 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1449 AN: 5168

South Asian (SAS) AF: 0.0143 AC: 69 AN: 4820

European-Finnish (FIN) AF: 0.0252 AC: 268 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00188 AC: 128 AN: 68032

Other (OTH) AF: 0.0345 AC: 73 AN: 2114

Alfa AF: 0.0195 Hom.: 52

Bravo AF: 0.0489

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs292932; hg19: chr16-72782824;