rs4771711

Positions:

• chr13-110850312-A-G

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 0.377 in 152,094 control chromosomes in the GnomAD database, including 12,641 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 0.38 (12641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.377 AC: 57369 AN: 151976 Hom.: 12636 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.377 AC: 57395 AN: 152094 Hom.: 12641 Cov.: 32 AF XY: 0.378 AC XY: 28106 AN XY: 74342

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.399

Alfa AF: 0.466 Hom.: 23861

Bravo AF: 0.362

Asia WGS AF: 0.182 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4771711; hg19: chr13-111502659;