1-109728085-T-C

Position:

• chr1-109728085-T-C

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 0.445 in 152,088 control chromosomes in the GnomAD database, including 15,681 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 0.44 (15681 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.109728085T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTM5	ENST00000429410.2	n.82+15737T>C		intron_variant		2
ENSG00000241720	ENST00000431955.1	n.249+2017T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67569 AN: 151970 Hom.: 15660 Cov.: 33

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.445 AC: 67631 AN: 152088 Hom.: 15681 Cov.: 33 AF XY: 0.444 AC XY: 33009 AN XY: 74342

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.442

Alfa AF: 0.421 Hom.: 1714

Bravo AF: 0.452

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.15
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11101996; hg19: chr1-110270707;