1-1329774-T-C

Variant names:

• chr1-1329774-T-C
• rs307355

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 0.811 in 152,250 control chromosomes in the GnomAD database, including 52,055 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 0.81 (52055 hom., cov: 37)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.27
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123335 AN: 152132 Hom.: 52039 Cov.: 37

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.811 AC: 123402 AN: 152250 Hom.: 52055 Cov.: 37 AF XY: 0.812 AC XY: 60437 AN XY: 74440

African (AFR) AF: 0.554 AC: 22998 AN: 41524

American (AMR) AF: 0.862 AC: 13186 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3159 AN: 3472

East Asian (EAS) AF: 0.813 AC: 4195 AN: 5160

South Asian (SAS) AF: 0.842 AC: 4067 AN: 4830

European-Finnish (FIN) AF: 0.876 AC: 9292 AN: 10612

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63628 AN: 68030

Other (OTH) AF: 0.828 AC: 1751 AN: 2116

Alfa AF: 0.866 Hom.: 7245

Bravo AF: 0.798

Asia WGS AF: 0.791 AC: 2754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs307355; hg19: chr1-1265154; COSMIC: COSV59566566;