11-127178464-T-C

Variant names:

• chr11-127178464-T-C
• rs1944828

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 0.118 in 152,104 control chromosomes in the GnomAD database, including 1,095 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 0.12 (1095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 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: 0.118 AC: 17915 AN: 151986 Hom.: 1092 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.118 AC: 17917 AN: 152104 Hom.: 1095 Cov.: 32 AF XY: 0.112 AC XY: 8340 AN XY: 74366

African (AFR) AF: 0.159 AC: 6606 AN: 41472

American (AMR) AF: 0.0953 AC: 1455 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 341 AN: 3470

East Asian (EAS) AF: 0.0570 AC: 295 AN: 5176

South Asian (SAS) AF: 0.0584 AC: 281 AN: 4810

European-Finnish (FIN) AF: 0.0702 AC: 744 AN: 10604

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.115 AC: 7795 AN: 67982

Other (OTH) AF: 0.125 AC: 264 AN: 2114

Alfa AF: 0.117 Hom.: 4020

Bravo AF: 0.122

Asia WGS AF: 0.0760 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.45
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1944828; hg19: chr11-127048359;