chr1-173496185-G-A

Position:

• chr1-173496185-G-A

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 0.211 in 152,040 control chromosomes in the GnomAD database, including 3,589 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 0.21 (3589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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 (EAS) allele frequency at 95% confidence interval = 0.301 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: 0.211 AC: 32010 AN: 151922 Hom.: 3579 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.211 AC: 32068 AN: 152040 Hom.: 3589 Cov.: 32 AF XY: 0.209 AC XY: 15512 AN XY: 74306

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.209

Alfa AF: 0.0868 Hom.: 96

Bravo AF: 0.220

Asia WGS AF: 0.210 AC: 729 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	1.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7529377; hg19: chr1-173465324;