chr11-127178638-T-C

Variant names:

• chr11-127178638-T-C
• rs1944827

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 0.535 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.560 AC: 23169 AN: 41408

American (AMR) AF: 0.498 AC: 7586 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3470

East Asian (EAS) AF: 0.155 AC: 803 AN: 5178

South Asian (SAS) AF: 0.509 AC: 2452 AN: 4818

European-Finnish (FIN) AF: 0.436 AC: 4592 AN: 10522

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38588 AN: 67940

Other (OTH) AF: 0.574 AC: 1212 AN: 2110

Alfa AF: 0.538 Hom.: 3945

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1944827; hg19: chr11-127048533;