11-128871844-T-C

Variant names:

• chr11-128871844-T-C
• rs7116606

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 0.7 in 152,078 control chromosomes in the GnomAD database, including 37,506 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 0.70 (37506 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 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: 0.700 AC: 106433 AN: 151960 Hom.: 37467 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.700 AC: 106515 AN: 152078 Hom.: 37506 Cov.: 33 AF XY: 0.705 AC XY: 52435 AN XY: 74346

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.701

Alfa AF: 0.711 Hom.: 40963

Bravo AF: 0.699

Asia WGS AF: 0.740 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7116606; hg19: chr11-128741739;