1-207103034-G-A

Position:

• chr1-207103034-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 0.103 in 152,136 control chromosomes in the GnomAD database, including 988 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 0.10 (988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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: 0.103 AC: 15681 AN: 152018 Hom.: 988 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0766

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.103 AC: 15689 AN: 152136 Hom.: 988 Cov.: 32 AF XY: 0.102 AC XY: 7622 AN XY: 74378

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0603

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0819 Hom.: 995

Bravo AF: 0.106

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11120211; hg19: chr1-207276379;