1-161538827-A-G

Position:

• chr1-161538827-A-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 0.282 in 151,918 control chromosomes in the GnomAD database, including 6,507 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 0.28 (6507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 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: 0.282 AC: 42827 AN: 151800 Hom.: 6502 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.282 AC: 42849 AN: 151918 Hom.: 6507 Cov.: 32 AF XY: 0.282 AC XY: 20973 AN XY: 74244

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.307

Alfa AF: 0.301 Hom.: 917

Bravo AF: 0.278

Asia WGS AF: 0.321 AC: 1116 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10919543; hg19: chr1-161508617;