1-208007808-A-G

Variant names:

• chr1-208007808-A-G
• rs631802

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 0.886 in 152,272 control chromosomes in the GnomAD database, including 59,902 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 0.89 (59902 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.886 AC: 134852 AN: 152154 Hom.: 59874 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.886 AC: 134933 AN: 152272 Hom.: 59902 Cov.: 33 AF XY: 0.885 AC XY: 65900 AN XY: 74436

African (AFR) AF: 0.870 AC: 36144 AN: 41548

American (AMR) AF: 0.862 AC: 13190 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3356 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5148 AN: 5188

South Asian (SAS) AF: 0.927 AC: 4466 AN: 4820

European-Finnish (FIN) AF: 0.852 AC: 9020 AN: 10592

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60672 AN: 68034

Other (OTH) AF: 0.903 AC: 1909 AN: 2114

Alfa AF: 0.874 Hom.: 7311

Bravo AF: 0.887

Asia WGS AF: 0.944 AC: 3284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.3
DANN	Benign	0.79
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs631802; hg19: chr1-208181153;