rs11705701

chr3-185826521-G-Achr3-185826521-G-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 0.538 in 152,104 control chromosomes in the GnomAD database, including 24,350 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 0.54 (24350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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: 0.538 AC: 81762 AN: 151986 Hom.: 24296 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.538 AC: 81882 AN: 152104 Hom.: 24350 Cov.: 32 AF XY: 0.532 AC XY: 39565 AN XY: 74356

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.512

Alfa AF: 0.462 Hom.: 16909

Bravo AF: 0.542

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	13
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11705701; hg19: chr3-185544309;