rs7668883

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377329	XR_007058467.1	n.301+9941A>G		intron_variant	Intron 2 of 3
LOC105377329	XR_007058468.1	n.301+9941A>G		intron_variant	Intron 2 of 3
LOC105377329	XR_007058469.1	n.301+9941A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251095	ENST00000506864.5	n.335+9941A>G		intron_variant	Intron 2 of 3	4
ENSG00000251095	ENST00000508021.5	n.190+9941A>G		intron_variant	Intron 2 of 4	4
ENSG00000251095	ENST00000509723.1	n.32+9941A>G		intron_variant	Intron 1 of 5	3

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 v4.3

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;