chr1-147849353-A-G

Position:

• chr1-147849353-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 0.0231 in 152,352 control chromosomes in the GnomAD database, including 56 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 0.023 (56 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0731 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: 0.0231 AC: 3511 AN: 152234 Hom.: 56 Cov.: 32

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.0796

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0181

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

GnomAD4 genome AF: 0.0231 AC: 3523 AN: 152352 Hom.: 56 Cov.: 32 AF XY: 0.0241 AC XY: 1799 AN XY: 74510

Gnomad4 AFR AF: 0.0284

Gnomad4 AMR AF: 0.0182

Gnomad4 ASJ AF: 0.00835

Gnomad4 EAS AF: 0.0794

Gnomad4 SAS AF: 0.0482

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.0167

Gnomad4 OTH AF: 0.0203

Alfa AF: 0.0182 Hom.: 2

Bravo AF: 0.0228

Asia WGS AF: 0.0780 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.0
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7554500; hg19: chr1-147321489;