rs10958357

Variant names:

• chr8-53407913-C-T
• rs10958357
• ENST00000521558.2:n.363-11847G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521558.2(ENSG00000253369):​n.363-11847G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,114 control chromosomes in the GnomAD database, including 23,816 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 0.53 (23816 hom., cov: 32)
• Consequence: ENSG00000253369 ENST00000521558.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

Genes affected

ENSG00000253369 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 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
ENSG00000253369	ENST00000521558.2	n.363-11847G>A		intron_variant	Intron 3 of 4	3
ENSG00000253369	ENST00000653042.1	n.534-6344G>A		intron_variant	Intron 4 of 6
ENSG00000253369	ENST00000653150.2	n.508-6344G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81287 AN: 151996 Hom.: 23810 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.535 AC: 81328 AN: 152114 Hom.: 23816 Cov.: 32 AF XY: 0.537 AC XY: 39969 AN XY: 74374

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.569

Alfa AF: 0.637 Hom.: 63979

Bravo AF: 0.522

Asia WGS AF: 0.633 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10958357; hg19: chr8-54320473;