chr8-20012165-G-A

Variant names:

• chr8-20012165-G-A
• rs1919484

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 0.228 in 152,064 control chromosomes in the GnomAD database, including 4,142 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 0.23 (4142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.228 AC: 34647 AN: 151946 Hom.: 4144 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.228 AC: 34638 AN: 152064 Hom.: 4142 Cov.: 32 AF XY: 0.228 AC XY: 16911 AN XY: 74328

African (AFR) AF: 0.146 AC: 6072 AN: 41480

American (AMR) AF: 0.232 AC: 3546 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1069 AN: 5178

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4818

European-Finnish (FIN) AF: 0.249 AC: 2627 AN: 10568

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18241 AN: 67972

Other (OTH) AF: 0.234 AC: 494 AN: 2112

Alfa AF: 0.212 Hom.: 1216

Bravo AF: 0.222

Asia WGS AF: 0.233 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.0
DANN	Benign	0.72
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1919484; hg19: chr8-19869676;