1-64695950-T-C

Variant names:

• chr1-64695950-T-C
• rs2148323

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 0.273 in 152,036 control chromosomes in the GnomAD database, including 7,073 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 0.27 (7073 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• 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 = 0.646 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: 0.272 AC: 41382 AN: 151918 Hom.: 7059 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.273 AC: 41441 AN: 152036 Hom.: 7073 Cov.: 32 AF XY: 0.279 AC XY: 20715 AN XY: 74298

African (AFR) AF: 0.411 AC: 17042 AN: 41438

American (AMR) AF: 0.313 AC: 4784 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3466

East Asian (EAS) AF: 0.665 AC: 3425 AN: 5154

South Asian (SAS) AF: 0.294 AC: 1415 AN: 4812

European-Finnish (FIN) AF: 0.254 AC: 2684 AN: 10584

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10664 AN: 67984

Other (OTH) AF: 0.264 AC: 555 AN: 2104

Alfa AF: 0.188 Hom.: 5506

Bravo AF: 0.292

Asia WGS AF: 0.488 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.47
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs2148323; hg19: chr1-65161633;