rs11955686

Positions:

• chr5-69444826-A-C
• chr5-69444826-A-G
• chr5-69444826-A-T

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 0.876 in 152,224 control chromosomes in the GnomAD database, including 59,756 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 0.88 (59756 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

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 (NFE) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133236 AN: 152104 Hom.: 59738 Cov.: 33

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.876 AC: 133300 AN: 152224 Hom.: 59756 Cov.: 33 AF XY: 0.877 AC XY: 65275 AN XY: 74450

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.968

Gnomad4 OTH AF: 0.904

Alfa AF: 0.947 Hom.: 49554

Bravo AF: 0.861

Asia WGS AF: 0.906 AC: 3150 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	2.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11955686; hg19: chr5-68740653;