1-109733122-A-G

Position:

• chr1-109733122-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 0.275 in 152,134 control chromosomes in the GnomAD database, including 7,173 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 (7173 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.109733122A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTM5	ENST00000429410.2	n.82+20774A>G		intron_variant		2
ENSG00000241720	ENST00000431955.1	n.425+772A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41737 AN: 152016 Hom.: 7165 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.275 AC: 41772 AN: 152134 Hom.: 7173 Cov.: 32 AF XY: 0.278 AC XY: 20692 AN XY: 74352

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.289

Alfa AF: 0.306 Hom.: 9847

Bravo AF: 0.270

Asia WGS AF: 0.511 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927328; hg19: chr1-110275744; COSMIC: COSV56661875;