rs11155996

Positions:

• chr6-154643016-G-A

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 0.341 in 150,310 control chromosomes in the GnomAD database, including 10,213 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 0.34 (10213 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51260 AN: 150194 Hom.: 10201 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.295

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.341 AC: 51311 AN: 150310 Hom.: 10213 Cov.: 31 AF XY: 0.339 AC XY: 24876 AN XY: 73292

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.361

Alfa AF: 0.329 Hom.: 2780

Bravo AF: 0.337

Asia WGS AF: 0.266 AC: 926 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
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: rs11155996; hg19: chr6-154964150;