chr1-158175439-T-C

Position:

• chr1-158175439-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 0.121 in 152,272 control chromosomes in the GnomAD database, including 1,553 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 0.12 (1553 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 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: 0.121 AC: 18360 AN: 152154 Hom.: 1546 Cov.: 33

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0971

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.121 AC: 18389 AN: 152272 Hom.: 1553 Cov.: 33 AF XY: 0.127 AC XY: 9439 AN XY: 74454

Gnomad4 AFR AF: 0.0932

Gnomad4 AMR AF: 0.0973

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0979

Alfa AF: 0.104 Hom.: 151

Bravo AF: 0.115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1570699; hg19: chr1-158145229;