rs4771711

Variant names:

• chr13-110850312-A-G
• rs4771711

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.157 AC: 6506 AN: 41486

American (AMR) AF: 0.445 AC: 6794 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3472

East Asian (EAS) AF: 0.129 AC: 667 AN: 5186

South Asian (SAS) AF: 0.266 AC: 1281 AN: 4808

European-Finnish (FIN) AF: 0.528 AC: 5590 AN: 10580

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33961 AN: 67978

Other (OTH) AF: 0.399 AC: 842 AN: 2112

Alfa AF: 0.446 Hom.: 52320

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4771711; hg19: chr13-111502659;