rs614080

Variant names:

• chr11-67579816-G-A
• rs614080

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 0.4 in 152,054 control chromosomes in the GnomAD database, including 14,432 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 0.40 (14432 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 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: 0.400 AC: 60818 AN: 151936 Hom.: 14434 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.400 AC: 60822 AN: 152054 Hom.: 14432 Cov.: 31 AF XY: 0.411 AC XY: 30535 AN XY: 74318

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.445

Alfa AF: 0.491 Hom.: 37394

Bravo AF: 0.378

Asia WGS AF: 0.602 AC: 2092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs614080; hg19: chr11-67347287;