1-12624318-C-T

Variant names:

• chr1-12624318-C-T
• rs3010931

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 0.097 in 151,934 control chromosomes in the GnomAD database, including 1,441 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 0.097 (1441 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 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: 0.0968 AC: 14693 AN: 151816 Hom.: 1432 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0793

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.00945

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0776

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

GnomAD4 genome AF: 0.0970 AC: 14737 AN: 151934 Hom.: 1441 Cov.: 31 AF XY: 0.0936 AC XY: 6954 AN XY: 74260

African (AFR) AF: 0.253 AC: 10442 AN: 41352

American (AMR) AF: 0.0465 AC: 710 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 214 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5184

South Asian (SAS) AF: 0.0823 AC: 395 AN: 4802

European-Finnish (FIN) AF: 0.00945 AC: 100 AN: 10584

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0385 AC: 2613 AN: 67958

Other (OTH) AF: 0.0777 AC: 164 AN: 2110

Alfa AF: 0.0534 Hom.: 699

Bravo AF: 0.105

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs3010931; hg19: chr1-12684324;