1-109726566-C-T

Position:

• chr1-109726566-C-T

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 0.0584 in 152,286 control chromosomes in the GnomAD database, including 388 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 0.058 (388 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.109726566C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTM5	ENST00000429410.2	n.82+14218C>T		intron_variant		2
ENSG00000241720	ENST00000431955.1	n.249+498C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0584 AC: 8883 AN: 152168 Hom.: 383 Cov.: 33

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0584 AC: 8897 AN: 152286 Hom.: 388 Cov.: 33 AF XY: 0.0591 AC XY: 4399 AN XY: 74452

Gnomad4 AFR AF: 0.0139

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.0328

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0583

Alfa AF: 0.0475 Hom.: 41

Bravo AF: 0.0594

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11101993; hg19: chr1-110269188;