chr1-212415353-G-A

Position:

• chr1-212415353-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 0.258 in 152,148 control chromosomes in the GnomAD database, including 6,821 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 0.26 (6821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

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 (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.258 AC: 39161 AN: 152030 Hom.: 6801 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.258 AC: 39218 AN: 152148 Hom.: 6821 Cov.: 32 AF XY: 0.252 AC XY: 18726 AN XY: 74408

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.245

Alfa AF: 0.213 Hom.: 687

Bravo AF: 0.266

Asia WGS AF: 0.142 AC: 494 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	1.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7533689; hg19: chr1-212588695;