rs11723705

Positions:

• chr4-54884905-T-C

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 0.821 in 152,190 control chromosomes in the GnomAD database, including 51,553 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 0.82 (51553 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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: 0.821 AC: 124891 AN: 152072 Hom.: 51502 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.821 AC: 125002 AN: 152190 Hom.: 51553 Cov.: 32 AF XY: 0.826 AC XY: 61444 AN XY: 74406

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.875

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.803

Alfa AF: 0.791 Hom.: 23790

Bravo AF: 0.825

Asia WGS AF: 0.902 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11723705; hg19: chr4-55751071;