rs619689

chr11-114456232-C-Gchr11-114456232-C-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 0.573 in 151,820 control chromosomes in the GnomAD database, including 25,500 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 0.57 (25500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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: 0.573 AC: 86934 AN: 151702 Hom.: 25451 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.573 AC: 87038 AN: 151820 Hom.: 25500 Cov.: 32 AF XY: 0.572 AC XY: 42409 AN XY: 74184

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.566

Alfa AF: 0.397 Hom.: 1000

Bravo AF: 0.583

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.78
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: rs619689; hg19: chr11-114326954;