rs1944827

Variant names:

• chr11-127178638-T-C
• rs1944827

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 0.535 in 151,894 control chromosomes in the GnomAD database, including 22,338 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 0.54 (22338 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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: 0.535 AC: 81259 AN: 151776 Hom.: 22323 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.535 AC: 81305 AN: 151894 Hom.: 22338 Cov.: 31 AF XY: 0.525 AC XY: 38987 AN XY: 74204

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.574

Alfa AF: 0.538 Hom.: 3833

Bravo AF: 0.538

Asia WGS AF: 0.357 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1944827; hg19: chr11-127048533;