1-234698385-A-G

Variant names:

• chr1-234698385-A-G
• rs11587639

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 0.0492 in 151,412 control chromosomes in the GnomAD database, including 211 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 0.049 (211 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0492 AC: 7437 AN: 151294 Hom.: 210 Cov.: 30

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.0584

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0395

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

GnomAD4 genome AF: 0.0492 AC: 7456 AN: 151412 Hom.: 211 Cov.: 30 AF XY: 0.0496 AC XY: 3668 AN XY: 73924

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.0677

Gnomad4 ASJ AF: 0.0210

Gnomad4 EAS AF: 0.0611

Gnomad4 SAS AF: 0.0317

Gnomad4 FIN AF: 0.0563

Gnomad4 NFE AF: 0.0459

Gnomad4 OTH AF: 0.0391

Alfa AF: 0.0505 Hom.: 37

Bravo AF: 0.0514

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11587639; hg19: chr1-234834132;