11-127629856-T-C

Variant names:

• chr11-127629856-T-C
• rs7928097

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 0.206 in 152,074 control chromosomes in the GnomAD database, including 4,043 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 0.21 (4043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 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: 0.206 AC: 31264 AN: 151956 Hom.: 4037 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0964

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.206 AC: 31306 AN: 152074 Hom.: 4043 Cov.: 32 AF XY: 0.208 AC XY: 15446 AN XY: 74324

African (AFR) AF: 0.371 AC: 15378 AN: 41472

American (AMR) AF: 0.103 AC: 1571 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3470

East Asian (EAS) AF: 0.0964 AC: 499 AN: 5176

South Asian (SAS) AF: 0.150 AC: 723 AN: 4820

European-Finnish (FIN) AF: 0.229 AC: 2419 AN: 10558

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9764 AN: 67988

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.151 Hom.: 2583

Bravo AF: 0.207

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.62
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7928097; hg19: chr11-127499751;