1-175060796-T-G

Variant names:

• chr1-175060796-T-G
• rs6672099

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 0.42 in 151,968 control chromosomes in the GnomAD database, including 13,831 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 0.42 (13831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 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: 0.420 AC: 63828 AN: 151850 Hom.: 13806 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.420 AC: 63895 AN: 151968 Hom.: 13831 Cov.: 32 AF XY: 0.424 AC XY: 31500 AN XY: 74280

African (AFR) AF: 0.340 AC: 14092 AN: 41444

American (AMR) AF: 0.409 AC: 6239 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1798 AN: 3464

East Asian (EAS) AF: 0.569 AC: 2936 AN: 5164

South Asian (SAS) AF: 0.528 AC: 2545 AN: 4816

European-Finnish (FIN) AF: 0.445 AC: 4698 AN: 10554

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30151 AN: 67954

Other (OTH) AF: 0.428 AC: 900 AN: 2102

Alfa AF: 0.432 Hom.: 39169

Bravo AF: 0.413

Asia WGS AF: 0.573 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.52
PhyloP100		0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6672099;

hg19: chr1-175029932;