1-204821849-A-G

Position:

• chr1-204821849-A-G

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 0.241 in 152,040 control chromosomes in the GnomAD database, including 6,991 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 0.24 (6991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 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: 0.240 AC: 36525 AN: 151922 Hom.: 6959 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.241 AC: 36614 AN: 152040 Hom.: 6991 Cov.: 32 AF XY: 0.249 AC XY: 18471 AN XY: 74312

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.0922

Gnomad4 OTH AF: 0.221

Alfa AF: 0.150 Hom.: 504

Bravo AF: 0.270

Asia WGS AF: 0.450 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2065160; hg19: chr1-204790977;