rs10399805

chr1-203186870-G-Achr1-203186870-G-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 0.176 in 574,560 control chromosomes in the GnomAD database, including 11,758 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 0.22 (4964 hom., cov: 32)
  • Exomes 𝑓: 0.16 (6794 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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: 0.222 AC: 33798 AN: 151928 Hom.: 4944 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0689

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.222

GnomAD4 exome AF: 0.159 AC: 67083 AN: 422512 Hom.: 6794 AF XY: 0.157 AC XY: 34740 AN XY: 221602

Gnomad4 AFR exome AF: 0.397

Gnomad4 AMR exome AF: 0.328

Gnomad4 ASJ exome AF: 0.185

Gnomad4 EAS exome AF: 0.314

Gnomad4 SAS exome AF: 0.144

Gnomad4 FIN exome AF: 0.0723

Gnomad4 NFE exome AF: 0.126

Gnomad4 OTH exome AF: 0.175

GnomAD4 genome AF: 0.222 AC: 33830 AN: 152048 Hom.: 4964 Cov.: 32 AF XY: 0.222 AC XY: 16490 AN XY: 74328

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0689

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.220

Alfa AF: 0.0463 Hom.: 57

Bravo AF: 0.253

Asia WGS AF: 0.219 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.7
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10399805; hg19: chr1-203155998;