1-153699771-G-T

Position:

• chr1-153699771-G-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 0.609 in 151,824 control chromosomes in the GnomAD database, including 28,982 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 0.61 (28982 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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: 0.608 AC: 92272 AN: 151704 Hom.: 28930 Cov.: 30

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.609 AC: 92388 AN: 151824 Hom.: 28982 Cov.: 30 AF XY: 0.609 AC XY: 45187 AN XY: 74184

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.590

Alfa AF: 0.563 Hom.: 14337

Bravo AF: 0.630

Asia WGS AF: 0.656 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7541193; hg19: chr1-153672247;