chr1-209809986-A-G

Variant names:

• chr1-209809986-A-G
• rs764093

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 0.276 in 152,102 control chromosomes in the GnomAD database, including 7,185 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 0.28 (7185 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 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: 0.276 AC: 41915 AN: 151984 Hom.: 7169 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.276 AC: 41970 AN: 152102 Hom.: 7185 Cov.: 32 AF XY: 0.277 AC XY: 20595 AN XY: 74388

African (AFR) AF: 0.443 AC: 18373 AN: 41458

American (AMR) AF: 0.348 AC: 5313 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3468

East Asian (EAS) AF: 0.476 AC: 2457 AN: 5166

South Asian (SAS) AF: 0.309 AC: 1487 AN: 4814

European-Finnish (FIN) AF: 0.127 AC: 1349 AN: 10608

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11747 AN: 67984

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.164 Hom.: 898

Bravo AF: 0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.45
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs764093; hg19: chr1-209983331; COSMIC: COSV65418987;