rs7846606

Variant names:

• chr8-76595378-A-G
• rs7846606
• ENST00000522961.2:n.230+87674T>C

Variant summary

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

The ENST00000814135.1(ZFHX4-AS1):​n.345+1957T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,050 control chromosomes in the GnomAD database, including 5,637 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 0.26 (5637 hom., cov: 32)
• Consequence: ZFHX4-AS1 ENST00000814135.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 5 publications found

Genes affected

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

LOC107986952 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814135.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFHX4-AS1	ENST00000522961.2	TSL:5	n.230+87674T>C		intron	N/A
	ZFHX4-AS1	ENST00000814135.1		n.345+1957T>C		intron	N/A
	ZFHX4-AS1	ENST00000814136.1		n.345+1957T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39992 AN: 151930 Hom.: 5612 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.263 AC: 40062 AN: 152050 Hom.: 5637 Cov.: 32 AF XY: 0.263 AC XY: 19577 AN XY: 74350

African (AFR) AF: 0.379 AC: 15703 AN: 41462

American (AMR) AF: 0.226 AC: 3457 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1374 AN: 5166

South Asian (SAS) AF: 0.263 AC: 1270 AN: 4820

European-Finnish (FIN) AF: 0.219 AC: 2320 AN: 10570

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14308 AN: 67968

Other (OTH) AF: 0.254 AC: 538 AN: 2114

Alfa AF: 0.227 Hom.: 14895

Bravo AF: 0.269

Asia WGS AF: 0.304 AC: 1056 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.54
PhyloP100		-0.0090

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7846606;

hg19: chr8-77507613;