rs6602318

Positions:

• chr10-8511107-C-T

Variant summary

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

The variant allele was found at a frequency of 0.489 in 152,080 control chromosomes in the GnomAD database, including 18,328 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 0.49 (18328 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74329 AN: 151962 Hom.: 18322 Cov.: 33

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.489 AC: 74371 AN: 152080 Hom.: 18328 Cov.: 33 AF XY: 0.485 AC XY: 36085 AN XY: 74330

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.469

Alfa AF: 0.491 Hom.: 8748

Bravo AF: 0.495

Asia WGS AF: 0.402 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.14
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6602318; hg19: chr10-8553070;