1-73952754-T-G

Variant names:

• chr1-73952754-T-G
• rs1417259

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 0.275 in 151,916 control chromosomes in the GnomAD database, including 6,558 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 0.28 (6558 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 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: 0.275 AC: 41811 AN: 151798 Hom.: 6560 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.275 AC: 41811 AN: 151916 Hom.: 6558 Cov.: 32 AF XY: 0.268 AC XY: 19860 AN XY: 74232

African (AFR) AF: 0.144 AC: 5961 AN: 41512

American (AMR) AF: 0.293 AC: 4468 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3466

East Asian (EAS) AF: 0.0740 AC: 380 AN: 5134

South Asian (SAS) AF: 0.202 AC: 973 AN: 4824

European-Finnish (FIN) AF: 0.257 AC: 2715 AN: 10558

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25047 AN: 67878

Other (OTH) AF: 0.297 AC: 626 AN: 2110

Alfa AF: 0.217 Hom.: 595

Bravo AF: 0.272

Asia WGS AF: 0.127 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.30
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1417259; hg19: chr1-74418437; COSMIC: COSV53379184;