11-69800079-T-C

Variant names:

• chr11-69800079-T-C
• rs4631909

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 0.482 in 152,120 control chromosomes in the GnomAD database, including 18,003 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 0.48 (18003 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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: 0.482 AC: 73198 AN: 152002 Hom.: 17987 Cov.: 33

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.482 AC: 73267 AN: 152120 Hom.: 18003 Cov.: 33 AF XY: 0.483 AC XY: 35918 AN XY: 74370

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.458

Alfa AF: 0.449 Hom.: 27764

Bravo AF: 0.475

Asia WGS AF: 0.492 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4631909; hg19: chr11-69614847;