chr20-4462943-T-C

Variant names:

• chr20-4462943-T-C
• rs297675

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.203 AC: 8432 AN: 41516

American (AMR) AF: 0.331 AC: 5050 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1322 AN: 5170

South Asian (SAS) AF: 0.174 AC: 841 AN: 4820

European-Finnish (FIN) AF: 0.199 AC: 2115 AN: 10604

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14329 AN: 67994

Other (OTH) AF: 0.228 AC: 483 AN: 2114

Alfa AF: 0.210 Hom.: 660

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs297675; hg19: chr20-4443590;