rs768586

Positions:

• chr1-34709225-T-C
• chr1-34709225-T-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 0.186 in 152,092 control chromosomes in the GnomAD database, including 2,951 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 0.19 (2951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 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: 0.186 AC: 28236 AN: 151974 Hom.: 2948 Cov.: 32

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.186 AC: 28258 AN: 152092 Hom.: 2951 Cov.: 32 AF XY: 0.185 AC XY: 13735 AN XY: 74358

Gnomad4 AFR AF: 0.0892

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.188

Alfa AF: 0.169 Hom.: 564

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs768586; hg19: chr1-35174826;