4-89597881-A-G

Variant names:

• chr4-89597881-A-G
• rs7668883
• ENST00000506864.5:n.335+9941A>G

Variant summary

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

The ENST00000506864.5(ENSG00000251095):​n.335+9941A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,184 control chromosomes in the GnomAD database, including 4,860 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 0.16 (4860 hom., cov: 32)
• Consequence: ENSG00000251095 ENST00000506864.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 1 publications found

Genes affected

ENSG00000251095 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506864.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251095	ENST00000506864.5	TSL:4	n.335+9941A>G		intron	N/A
	ENSG00000251095	ENST00000508021.5	TSL:4	n.190+9941A>G		intron	N/A
	ENSG00000251095	ENST00000509723.1	TSL:3	n.32+9941A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24714 AN: 152066 Hom.: 4839 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0758

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0397

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.163 AC: 24772 AN: 152184 Hom.: 4860 Cov.: 32 AF XY: 0.159 AC XY: 11834 AN XY: 74418

African (AFR) AF: 0.474 AC: 19667 AN: 41472

American (AMR) AF: 0.0756 AC: 1155 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0393 AC: 190 AN: 4830

European-Finnish (FIN) AF: 0.0362 AC: 384 AN: 10618

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0428 AC: 2909 AN: 68012

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.0787 Hom.: 822

Bravo AF: 0.178

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.39
DANN	Benign	0.87
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs7668883; hg19: chr4-90519032;