rs7443800

Variant names:

• chr5-176132836-G-A
• rs7443800
• ENST00000697530.1:n.1220-4325G>A

Variant summary

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

The ENST00000697530.1(ENSG00000289731):​n.1220-4325G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,332 control chromosomes in the GnomAD database, including 9,276 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 0.32 (9276 hom., cov: 29)
• Consequence: ENSG00000289731 ENST00000697530.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 17 publications found

Genes affected

ENSG00000289731 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697530.1. 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
	ENSG00000289731	ENST00000697530.1		n.1220-4325G>A		intron	N/A
	ENSG00000289731	ENST00000697531.1		n.655-4325G>A		intron	N/A
	ENSG00000289731	ENST00000697534.1		n.622-4325G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49035 AN: 151210 Hom.: 9275 Cov.: 29

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.324 AC: 49047 AN: 151332 Hom.: 9276 Cov.: 29 AF XY: 0.324 AC XY: 23936 AN XY: 73946

African (AFR) AF: 0.125 AC: 5141 AN: 41188

American (AMR) AF: 0.314 AC: 4779 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1325 AN: 3464

East Asian (EAS) AF: 0.338 AC: 1712 AN: 5064

South Asian (SAS) AF: 0.296 AC: 1415 AN: 4782

European-Finnish (FIN) AF: 0.457 AC: 4813 AN: 10542

Middle Eastern (MID) AF: 0.358 AC: 103 AN: 288

European-Non Finnish (NFE) AF: 0.422 AC: 28612 AN: 67782

Other (OTH) AF: 0.338 AC: 712 AN: 2106

Alfa AF: 0.387 Hom.: 12946

Bravo AF: 0.306

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.56
PhyloP100		0.14

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: rs7443800;

hg19: chr5-175559839;