1-205137154-A-G

Position:

• chr1-205137154-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 0.803 in 151,732 control chromosomes in the GnomAD database, including 50,453 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 0.80 (50453 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121744 AN: 151614 Hom.: 50439 Cov.: 31

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.803 AC: 121794 AN: 151732 Hom.: 50453 Cov.: 31 AF XY: 0.808 AC XY: 59920 AN XY: 74198

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.844

Alfa AF: 0.837 Hom.: 9159

Bravo AF: 0.793

Asia WGS AF: 0.931 AC: 3234 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
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: rs10900451; hg19: chr1-205106282;