rs11726248

Positions:

• chr4-170132368-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 0.0674 in 152,226 control chromosomes in the GnomAD database, including 494 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 0.067 (494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 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: 0.0675 AC: 10261 AN: 152108 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0674 AC: 10262 AN: 152226 Hom.: 494 Cov.: 32 AF XY: 0.0633 AC XY: 4713 AN XY: 74414

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0675

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0505

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0794

Alfa AF: 0.0807 Hom.: 76

Bravo AF: 0.0668

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.8
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11726248; hg19: chr4-171053519;