11-69804649-A-G

Variant names:

• chr11-69804649-A-G
• rs4980700

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 0.539 in 152,102 control chromosomes in the GnomAD database, including 22,369 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 (22369 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 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: 0.539 AC: 81975 AN: 151984 Hom.: 22353 Cov.: 34

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.539 AC: 82040 AN: 152102 Hom.: 22369 Cov.: 34 AF XY: 0.541 AC XY: 40213 AN XY: 74342

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.513

Alfa AF: 0.530 Hom.: 37355

Bravo AF: 0.524

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4980700; hg19: chr11-69619417;