chr1-87599174-G-A

Variant names:

• chr1-87599174-G-A
• rs72953990

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 0.131 in 151,810 control chromosomes in the GnomAD database, including 1,399 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 0.13 (1399 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19816 AN: 151694 Hom.: 1400 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.00465

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.131 AC: 19825 AN: 151810 Hom.: 1399 Cov.: 31 AF XY: 0.132 AC XY: 9814 AN XY: 74160

African (AFR) AF: 0.109 AC: 4507 AN: 41388

American (AMR) AF: 0.0938 AC: 1431 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3468

East Asian (EAS) AF: 0.00466 AC: 24 AN: 5152

South Asian (SAS) AF: 0.200 AC: 961 AN: 4806

European-Finnish (FIN) AF: 0.204 AC: 2140 AN: 10492

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9699 AN: 67938

Other (OTH) AF: 0.127 AC: 269 AN: 2110

Alfa AF: 0.142 Hom.: 334

Bravo AF: 0.117

Asia WGS AF: 0.0950 AC: 333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.52
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs72953990; hg19: chr1-88064857;