chr20-62704323-C-A

Variant names:

• chr20-62704323-C-A
• rs2427400

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 0.154 in 152,216 control chromosomes in the GnomAD database, including 1,986 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 0.15 (1986 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 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: 0.154 AC: 23474 AN: 152098 Hom.: 1987 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.154 AC: 23479 AN: 152216 Hom.: 1986 Cov.: 33 AF XY: 0.157 AC XY: 11653 AN XY: 74422

African (AFR) AF: 0.123 AC: 5127 AN: 41548

American (AMR) AF: 0.102 AC: 1556 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3470

East Asian (EAS) AF: 0.133 AC: 688 AN: 5174

South Asian (SAS) AF: 0.154 AC: 743 AN: 4818

European-Finnish (FIN) AF: 0.266 AC: 2821 AN: 10592

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11654 AN: 67994

Other (OTH) AF: 0.136 AC: 287 AN: 2112

Alfa AF: 0.160 Hom.: 378

Bravo AF: 0.141

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.45
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2427400; hg19: chr20-61335675;