rs4084127

Positions:

• chr11-69781755-G-A
• chr11-69781755-G-C

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 0.322 in 152,018 control chromosomes in the GnomAD database, including 8,455 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 0.32 (8455 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.444 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: 0.322 AC: 48906 AN: 151900 Hom.: 8439 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.322 AC: 48943 AN: 152018 Hom.: 8455 Cov.: 32 AF XY: 0.319 AC XY: 23697 AN XY: 74296

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.337

Alfa AF: 0.361 Hom.: 19014

Bravo AF: 0.331

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.078
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: rs4084127; hg19: chr11-69596523;