rs1374645

Positions:

• chr11-92940715-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 0.0853 in 152,118 control chromosomes in the GnomAD database, including 1,169 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 0.085 (1169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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: 0.0851 AC: 12933 AN: 152000 Hom.: 1162 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0648

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.0778

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

GnomAD4 genome AF: 0.0853 AC: 12982 AN: 152118 Hom.: 1169 Cov.: 32 AF XY: 0.0841 AC XY: 6255 AN XY: 74384

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0522

Gnomad4 ASJ AF: 0.0366

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.0221

Gnomad4 NFE AF: 0.0277

Gnomad4 OTH AF: 0.0770

Alfa AF: 0.0609 Hom.: 80

Bravo AF: 0.0941

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374645; hg19: chr11-92673881;