rs10958357

Positions:

• chr8-53407913-C-T

Variant summary

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

The ENST00000654917.2(ENSG00000253369):​n.491-11847G>A variant causes a intron, non coding transcript 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: ENST00000654917.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654917.2	n.491-11847G>A		intron_variant, non_coding_transcript_variant

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;