1-204821849-A-G

Variant names:

• chr1-204821849-A-G
• rs2065160

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 0.241 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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.408 AC: 16920 AN: 41430

American (AMR) AF: 0.374 AC: 5711 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4009 AN: 5174

South Asian (SAS) AF: 0.147 AC: 708 AN: 4812

European-Finnish (FIN) AF: 0.189 AC: 1998 AN: 10578

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.0922 AC: 6266 AN: 67980

Other (OTH) AF: 0.221 AC: 466 AN: 2104

Alfa AF: 0.147 Hom.: 520

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2065160; hg19: chr1-204790977;