1-153205376-C-T

Variant names:

• chr1-153205376-C-T
• rs7534334

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 0.254 in 151,986 control chromosomes in the GnomAD database, including 5,895 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 0.25 (5895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 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: 0.254 AC: 38565 AN: 151868 Hom.: 5897 Cov.: 32

Gnomad AFR AF: 0.0817

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.254 AC: 38559 AN: 151986 Hom.: 5895 Cov.: 32 AF XY: 0.253 AC XY: 18761 AN XY: 74266

African (AFR) AF: 0.0816 AC: 3381 AN: 41458

American (AMR) AF: 0.229 AC: 3496 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3470

East Asian (EAS) AF: 0.121 AC: 624 AN: 5156

South Asian (SAS) AF: 0.262 AC: 1260 AN: 4808

European-Finnish (FIN) AF: 0.391 AC: 4115 AN: 10532

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23441 AN: 67956

Other (OTH) AF: 0.262 AC: 555 AN: 2116

Alfa AF: 0.295 Hom.: 13138

Bravo AF: 0.234

Asia WGS AF: 0.176 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.026
DANN	Benign	0.50
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7534334; hg19: chr1-153177852;