chr1-150770224-T-C

Variant names:

• chr1-150770224-T-C
• rs11204725

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 0.413 in 151,650 control chromosomes in the GnomAD database, including 14,993 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 0.41 (14993 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.743
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.413 AC: 62613 AN: 151536 Hom.: 14994 Cov.: 30

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.413 AC: 62613 AN: 151650 Hom.: 14993 Cov.: 30 AF XY: 0.412 AC XY: 30518 AN XY: 74070

African (AFR) AF: 0.167 AC: 6890 AN: 41308

American (AMR) AF: 0.451 AC: 6868 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2147 AN: 5166

South Asian (SAS) AF: 0.328 AC: 1581 AN: 4818

European-Finnish (FIN) AF: 0.556 AC: 5817 AN: 10462

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36442 AN: 67914

Other (OTH) AF: 0.433 AC: 912 AN: 2104

Alfa AF: 0.502 Hom.: 31062

Bravo AF: 0.399

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.7
DANN	Benign	0.75
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs11204725; hg19: chr1-150742700;