rs297675

Variant names:

• chr20-4462943-T-C
• rs297675

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 0.22 in 152,166 control chromosomes in the GnomAD database, including 3,810 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 (3810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33512 AN: 152048 Hom.: 3803 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.220 AC: 33526 AN: 152166 Hom.: 3810 Cov.: 32 AF XY: 0.223 AC XY: 16566 AN XY: 74386

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.228

Alfa AF: 0.206 Hom.: 406

Bravo AF: 0.231

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
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: rs297675; hg19: chr20-4443590;