1-5110652-A-G

Position:

• chr1-5110652-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.145 in 152,270 control chromosomes in the GnomAD database, including 1,892 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 0.14 (1892 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21999 AN: 152152 Hom.: 1880 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0902

Gnomad EAS AF: 0.0732

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.145 AC: 22056 AN: 152270 Hom.: 1892 Cov.: 33 AF XY: 0.143 AC XY: 10638 AN XY: 74458

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0902

Gnomad4 EAS AF: 0.0730

Gnomad4 SAS AF: 0.0905

Gnomad4 FIN AF: 0.0818

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.117

Alfa AF: 0.108 Hom.: 2299

Bravo AF: 0.157

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7513590; hg19: chr1-5170712;