rs1074156

Positions:

• chr11-65690698-G-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 0.335 in 151,964 control chromosomes in the GnomAD database, including 8,874 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 (8874 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 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: 0.335 AC: 50942 AN: 151846 Hom.: 8869 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.335 AC: 50983 AN: 151964 Hom.: 8874 Cov.: 31 AF XY: 0.340 AC XY: 25214 AN XY: 74260

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.321

Alfa AF: 0.341 Hom.: 1515

Bravo AF: 0.313

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.56
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074156; hg19: chr11-65458169;