chr1-8312476-C-T

Variant names:

• chr1-8312476-C-T
• rs1107284

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 0.553 in 152,060 control chromosomes in the GnomAD database, including 25,107 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 0.55 (25107 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84046 AN: 151942 Hom.: 25102 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.553 AC: 84071 AN: 152060 Hom.: 25107 Cov.: 33 AF XY: 0.559 AC XY: 41521 AN XY: 74320

African (AFR) AF: 0.316 AC: 13102 AN: 41458

American (AMR) AF: 0.642 AC: 9815 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1880 AN: 3466

East Asian (EAS) AF: 0.754 AC: 3906 AN: 5178

South Asian (SAS) AF: 0.488 AC: 2351 AN: 4816

European-Finnish (FIN) AF: 0.732 AC: 7720 AN: 10552

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43398 AN: 67996

Other (OTH) AF: 0.542 AC: 1144 AN: 2110

Alfa AF: 0.593 Hom.: 14670

Bravo AF: 0.541

Asia WGS AF: 0.554 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.023
DANN	Benign	0.70
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1107284; hg19: chr1-8372536; COSMIC: COSV53275409;