16-72722202-G-T

Position:

• chr16-72722202-G-T

Variant summary

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

The ENST00000563328.4(ZFHX3-AS1):​n.165-23203G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,096 control chromosomes in the GnomAD database, including 3,628 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 0.19 (3628 hom., cov: 32)
• Consequence: ZFHX3-AS1 ENST00000563328.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414

Genes affected

ZFHX3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZFHX3-AS1	NR_171702.1	n.328+8213G>T		intron_variant
ZFHX3-AS1	NR_171703.1	n.285+8786G>T		intron_variant
ZFHX3-AS1	NR_171704.1	n.285+8786G>T		intron_variant
ZFHX3-AS1	NR_171705.1	n.202-23203G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZFHX3-AS1	ENST00000563328.4	n.165-23203G>T		intron_variant		3
ZFHX3-AS1	ENST00000653037.2	n.290+8786G>T		intron_variant
ZFHX3-AS1	ENST00000668995.1	n.338+8213G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29061 AN: 151978 Hom.: 3628 Cov.: 32

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.191 AC: 29053 AN: 152096 Hom.: 3628 Cov.: 32 AF XY: 0.187 AC XY: 13883 AN XY: 74354

Gnomad4 AFR AF: 0.0529

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0288

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.199

Alfa AF: 0.226 Hom.: 2329

Bravo AF: 0.181

Asia WGS AF: 0.0750 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500569; hg19: chr16-72756101;