rs4986894

Positions:

• chr10-94762608-T-C
• chr10-94762608-T-G

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 0.163 in 1,232,090 control chromosomes in the GnomAD database, including 18,650 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 0.17 (2341 hom., cov: 32)
  • Exomes 𝑓: 0.16 (16309 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 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: 0.166 AC: 25297 AN: 151964 Hom.: 2337 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.162 AC: 175358 AN: 1080008 Hom.: 16309 AF XY: 0.168 AC XY: 91270 AN XY: 544716

Gnomad4 AFR exome AF: 0.176

Gnomad4 AMR exome AF: 0.105

Gnomad4 ASJ exome AF: 0.133

Gnomad4 EAS exome AF: 0.302

Gnomad4 SAS exome AF: 0.323

Gnomad4 FIN exome AF: 0.173

Gnomad4 NFE exome AF: 0.144

Gnomad4 OTH exome AF: 0.164

GnomAD4 genome AF: 0.166 AC: 25314 AN: 152082 Hom.: 2341 Cov.: 32 AF XY: 0.171 AC XY: 12672 AN XY: 74318

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.152

Alfa AF: 0.141 Hom.: 1503

Bravo AF: 0.159

Asia WGS AF: 0.303 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4986894; hg19: chr10-96522365; COSMIC: COSV64908948;