rs3810608

Positions:

• chr22-21758505-G-A

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 0.175 in 152,214 control chromosomes in the GnomAD database, including 2,719 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 0.18 (2719 hom., cov: 31)
  • Exomes 𝑓: 0.11 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26625 AN: 151904 Hom.: 2715 Cov.: 31

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.0990

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.205

GnomAD4 exome AF: 0.115 AC: 22 AN: 192 Hom.: 0 Cov.: 0 AF XY: 0.127 AC XY: 17 AN XY: 134

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.120

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.175 AC: 26630 AN: 152022 Hom.: 2719 Cov.: 31 AF XY: 0.172 AC XY: 12786 AN XY: 74304

Gnomad4 AFR AF: 0.0837

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.0993

Gnomad4 SAS AF: 0.0998

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.203

Alfa AF: 0.195 Hom.: 466

Bravo AF: 0.171

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3810608; hg19: chr22-22112794; COSMIC: COSV53189787;