1-156886003-T-C

Variant names:

• chr1-156886003-T-C
• rs12564129

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 0.0955 in 152,270 control chromosomes in the GnomAD database, including 1,377 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 0.096 (1377 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811
• 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 (EAS) allele frequency at 95% confidence interval = 0.49 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: 0.0955 AC: 14528 AN: 152152 Hom.: 1378 Cov.: 33

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0955 AC: 14545 AN: 152270 Hom.: 1377 Cov.: 33 AF XY: 0.102 AC XY: 7611 AN XY: 74462

African (AFR) AF: 0.0989 AC: 4111 AN: 41554

American (AMR) AF: 0.130 AC: 1991 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3472

East Asian (EAS) AF: 0.506 AC: 2620 AN: 5174

South Asian (SAS) AF: 0.306 AC: 1479 AN: 4834

European-Finnish (FIN) AF: 0.0611 AC: 648 AN: 10612

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0478 AC: 3248 AN: 68008

Other (OTH) AF: 0.110 AC: 232 AN: 2114

Alfa AF: 0.0847 Hom.: 669

Bravo AF: 0.0983

Asia WGS AF: 0.378 AC: 1314 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	0.69
DANN	Benign	0.40
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs12564129; hg19: chr1-156855795;