1-156146697-T-G

Position:

• chr1-156146697-T-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 0.218 in 152,138 control chromosomes in the GnomAD database, including 4,600 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 0.22 (4600 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

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 (AMR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33182 AN: 152020 Hom.: 4594 Cov.: 32

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.218 AC: 33195 AN: 152138 Hom.: 4600 Cov.: 32 AF XY: 0.222 AC XY: 16490 AN XY: 74372

Gnomad4 AFR AF: 0.0524

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.248

Alfa AF: 0.270 Hom.: 8206

Bravo AF: 0.212

Asia WGS AF: 0.267 AC: 928 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	3.5
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468772; hg19: chr1-156116488;