rs4084127

Variant names:

• chr11-69781755-G-A
• rs4084127

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.226 AC: 9355 AN: 41474

American (AMR) AF: 0.453 AC: 6915 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3470

East Asian (EAS) AF: 0.159 AC: 824 AN: 5168

South Asian (SAS) AF: 0.308 AC: 1478 AN: 4806

European-Finnish (FIN) AF: 0.300 AC: 3167 AN: 10566

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24757 AN: 67946

Other (OTH) AF: 0.337 AC: 712 AN: 2110

Alfa AF: 0.353 Hom.: 39992

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
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs4084127; hg19: chr11-69596523;