1-175060411-A-T

Variant names:

• chr1-175060411-A-T
• rs1009418

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 0.972 in 152,032 control chromosomes in the GnomAD database, including 71,796 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 0.97 (71796 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.986 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: 0.972 AC: 147595 AN: 151916 Hom.: 71738 Cov.: 30

Gnomad AFR AF: 0.994

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.972 AC: 147711 AN: 152032 Hom.: 71796 Cov.: 30 AF XY: 0.973 AC XY: 72323 AN XY: 74324

African (AFR) AF: 0.994 AC: 41235 AN: 41486

American (AMR) AF: 0.977 AC: 14904 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3323 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5186 AN: 5188

South Asian (SAS) AF: 0.986 AC: 4757 AN: 4824

European-Finnish (FIN) AF: 0.956 AC: 10024 AN: 10490

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65120 AN: 67994

Other (OTH) AF: 0.965 AC: 2041 AN: 2114

Alfa AF: 0.967 Hom.: 8831

Bravo AF: 0.973

Asia WGS AF: 0.996 AC: 3442 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.80
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1009418; hg19: chr1-175029547;