chr1-1208277-C-G

Variant names:

• chr1-1208277-C-G
• rs3753348

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 0.0535 in 152,252 control chromosomes in the GnomAD database, including 254 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 0.054 (254 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0533 AC: 8108 AN: 152134 Hom.: 249 Cov.: 33

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0861

Gnomad FIN AF: 0.0576

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0469

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0535 AC: 8147 AN: 152252 Hom.: 254 Cov.: 33 AF XY: 0.0539 AC XY: 4013 AN XY: 74434

African (AFR) AF: 0.0558 AC: 2320 AN: 41558

American (AMR) AF: 0.0406 AC: 621 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3470

East Asian (EAS) AF: 0.142 AC: 735 AN: 5168

South Asian (SAS) AF: 0.0866 AC: 418 AN: 4826

European-Finnish (FIN) AF: 0.0576 AC: 611 AN: 10616

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0469 AC: 3189 AN: 67982

Other (OTH) AF: 0.0482 AC: 102 AN: 2114

Alfa AF: 0.0127 Hom.: 7

Bravo AF: 0.0517

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.23
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs3753348; hg19: chr1-1143657; COSMIC: COSV60775823;