rs6468953

Variant names:

• chr8-87666663-C-A
• rs6468953
• ENST00000440763.6:n.156-30013G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-87666663-C-A
• chr8-87666663-C-G
• chr8-87666663-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000517711.5(ENSG00000253500):​n.70-19634G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00528 in 152,026 control chromosomes in the GnomAD database, including 11 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 0.0053 (11 hom., cov: 32)
• Consequence: ENSG00000253500 ENST00000517711.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817

Genes affected

ENSG00000253500 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00528 (802/152026) while in subpopulation AFR AF= 0.0174 (720/41488). AF 95% confidence interval is 0.0163. There are 11 homozygotes in gnomad4. There are 360 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375626	XR_928380.2	n.123-1707C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253500	ENST00000440763.6	n.156-30013G>T		intron_variant	Intron 2 of 3	5
ENSG00000253500	ENST00000517711.5	n.70-19634G>T		intron_variant	Intron 1 of 3	3
ENSG00000253500	ENST00000518494.1	n.212-19634G>T		intron_variant	Intron 3 of 4	3
ENSG00000253500	ENST00000657849.1	n.81-30013G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00526 AC: 799 AN: 151906 Hom.: 11 Cov.: 32

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00315

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000294

Gnomad OTH AF: 0.00670

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

GnomAD4 genome AF: 0.00528 AC: 802 AN: 152026 Hom.: 11 Cov.: 32 AF XY: 0.00485 AC XY: 360 AN XY: 74296

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.00315

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000294

Gnomad4 OTH AF: 0.00664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.41
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6468953; hg19: chr8-88678891;