1-29814163-T-A

Variant names:

• chr1-29814163-T-A
• rs1074073

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 0.364 in 151,922 control chromosomes in the GnomAD database, including 10,478 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 0.36 (10478 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 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: 0.364 AC: 55237 AN: 151804 Hom.: 10473 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.364 AC: 55278 AN: 151922 Hom.: 10478 Cov.: 32 AF XY: 0.361 AC XY: 26771 AN XY: 74246

African (AFR) AF: 0.272 AC: 11293 AN: 41466

American (AMR) AF: 0.399 AC: 6089 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1771 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1077 AN: 5176

South Asian (SAS) AF: 0.400 AC: 1925 AN: 4814

European-Finnish (FIN) AF: 0.352 AC: 3697 AN: 10504

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28185 AN: 67914

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.383 Hom.: 1413

Bravo AF: 0.362

Asia WGS AF: 0.276 AC: 961 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.21
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1074073; hg19: chr1-30287010;