16-72722202-G-C

Variant names:

• chr16-72722202-G-C
• rs10500569
• ENST00000563328.5:n.203-23203G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000563328.5(ZFHX3-AS1):​n.203-23203G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ZFHX3-AS1 ENST00000563328.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFHX3-AS1	NR_171702.1	n.328+8213G>C		intron_variant	Intron 3 of 4
ZFHX3-AS1	NR_171703.1	n.285+8786G>C		intron_variant	Intron 2 of 4
ZFHX3-AS1	NR_171704.1	n.285+8786G>C		intron_variant	Intron 2 of 3
ZFHX3-AS1	NR_171705.1	n.202-23203G>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFHX3-AS1	ENST00000563328.5	n.203-23203G>C		intron_variant	Intron 1 of 4	3
ZFHX3-AS1	ENST00000653037.2	n.290+8786G>C		intron_variant	Intron 2 of 4
ZFHX3-AS1	ENST00000668995.1	n.338+8213G>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 10437

Bravo AF: 0.0000151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.59
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10500569; hg19: chr16-72756101;