rs10504630

Variant names:

• chr8-76624275-C-T
• rs10504630
• ENST00000518143.3:n.495-7824G>A

Variant summary

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

The ENST00000518143.3(ZFHX4-AS1):​n.495-7824G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0143 in 152,264 control chromosomes in the GnomAD database, including 72 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 0.014 (72 hom., cov: 31)
• Consequence: ZFHX4-AS1 ENST00000518143.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 1 publications found

Genes affected

ZFHX4-AS1 (HGNC:44165): (ZFHX4 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518143.3. 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
	ZFHX4-AS1	NR_024360.1		n.432-7824G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFHX4-AS1	ENST00000518143.3	TSL:1	n.495-7824G>A		intron	N/A
	ZFHX4-AS1	ENST00000522357.2	TSL:3	n.235-7824G>A		intron	N/A
	ZFHX4-AS1	ENST00000522961.2	TSL:5	n.230+58777G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0143 AC: 2180 AN: 152146 Hom.: 72 Cov.: 31

Gnomad AFR AF: 0.00251

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.00546

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0143 AC: 2178 AN: 152264 Hom.: 72 Cov.: 31 AF XY: 0.0159 AC XY: 1186 AN XY: 74450

African (AFR) AF: 0.00250 AC: 104 AN: 41556

American (AMR) AF: 0.0171 AC: 261 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3470

East Asian (EAS) AF: 0.134 AC: 693 AN: 5178

South Asian (SAS) AF: 0.0632 AC: 305 AN: 4826

European-Finnish (FIN) AF: 0.00546 AC: 58 AN: 10616

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

European-Non Finnish (NFE) AF: 0.0102 AC: 697 AN: 68014

Other (OTH) AF: 0.0180 AC: 38 AN: 2112

Alfa AF: 0.0105 Hom.: 6

Bravo AF: 0.0123

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.42
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10504630; hg19: chr8-77536510;