rs3767221

Positions:

• chr1-19975288-A-C

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 0.333 in 184,764 control chromosomes in the GnomAD database, including 11,437 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 0.33 (9057 hom., cov: 32)
  • Exomes 𝑓: 0.36 (2380 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 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: 0.326 AC: 49557 AN: 151854 Hom.: 9067 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.314

GnomAD4 exome AF: 0.364 AC: 11936 AN: 32792 Hom.: 2380 AF XY: 0.367 AC XY: 6259 AN XY: 17058

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.355

Gnomad4 ASJ exome AF: 0.353

Gnomad4 EAS exome AF: 0.266

Gnomad4 SAS exome AF: 0.385

Gnomad4 FIN exome AF: 0.406

Gnomad4 NFE exome AF: 0.394

Gnomad4 OTH exome AF: 0.360

GnomAD4 genome AF: 0.326 AC: 49551 AN: 151972 Hom.: 9057 Cov.: 32 AF XY: 0.332 AC XY: 24640 AN XY: 74264

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.313

Alfa AF: 0.342 Hom.: 1160

Bravo AF: 0.307

Asia WGS AF: 0.325 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3767221; hg19: chr1-20301781;