rs599957

Variant names:

• chr6-168704664-A-C
• rs599957
• ENST00000746859.1:n.308+7109A>C

Variant summary

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

The ENST00000746859.1(ENSG00000289090):​n.308+7109A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,234 control chromosomes in the GnomAD database, including 64,307 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 0.92 (64307 hom., cov: 32)
• Consequence: ENSG00000289090 ENST00000746859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 2 publications found

Genes affected

ENSG00000289090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289090	ENST00000746859.1	n.308+7109A>C		intron_variant	Intron 2 of 4
ENSG00000289090	ENST00000746861.1	n.282-5035A>C		intron_variant	Intron 2 of 2
ENSG00000289090	ENST00000746862.1	n.279-3813A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139820 AN: 152116 Hom.: 64277 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.919 AC: 139907 AN: 152234 Hom.: 64307 Cov.: 32 AF XY: 0.918 AC XY: 68349 AN XY: 74424

African (AFR) AF: 0.923 AC: 38339 AN: 41522

American (AMR) AF: 0.908 AC: 13898 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3171 AN: 3470

East Asian (EAS) AF: 0.961 AC: 4951 AN: 5154

South Asian (SAS) AF: 0.951 AC: 4590 AN: 4826

European-Finnish (FIN) AF: 0.920 AC: 9760 AN: 10614

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62087 AN: 68022

Other (OTH) AF: 0.931 AC: 1968 AN: 2114

Alfa AF: 0.916 Hom.: 37486

Bravo AF: 0.919

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.70
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs599957; hg19: chr6-169104792;