chr1-11865243-A-G

Position:

• chr1-11865243-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 0.417 in 152,088 control chromosomes in the GnomAD database, including 14,574 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 0.42 (14574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 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: 0.417 AC: 63301 AN: 151970 Hom.: 14536 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.417 AC: 63384 AN: 152088 Hom.: 14574 Cov.: 32 AF XY: 0.410 AC XY: 30494 AN XY: 74376

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.399

Alfa AF: 0.370 Hom.: 21838

Bravo AF: 0.420

Asia WGS AF: 0.368 AC: 1280 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	1.4
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6676300; hg19: chr1-11925300; COSMIC: COSV59923971;